From 1522810f7c0f5770000a9e0a97d81ca2e65ac76d Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Thu, 3 Apr 2025 14:49:03 +0200
Subject: [PATCH 01/14] feat(taillies): support reading option taillies record

---
 Cargo.lock                      | 42 +++++++++++----
 Cargo.toml                      |  2 +-
 core/Cargo.toml                 |  3 ++
 core/src/api.rs                 | 24 ++++-----
 core/src/datamodel/_impl.rs     | 91 ++++++++++++++++++---------------
 core/src/datamodel/main_file.rs | 74 +++++++++++++++++++++------
 core/src/datamodel/mod.rs       |  4 +-
 core/src/impl_concat.rs         |  7 ++-
 core/src/impl_unique.rs         |  5 +-
 examples/example_rust.rs        | 18 ++++---
 examples/out.html               |  2 +-
 examples/out.svg                |  2 +-
 12 files changed, 180 insertions(+), 94 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index c75ba1e..c2c54f4 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -81,10 +81,13 @@ dependencies = [
 
 [[package]]
 name = "bcore"
-version = "0.3.4"
+version = "0.4.1"
 dependencies = [
+ "csv",
  "hdf5",
  "ndarray 0.16.1",
+ "serde",
+ "serde_json",
  "thiserror 2.0.11",
 ]
 
@@ -243,6 +246,27 @@ dependencies = [
  "typenum",
 ]
 
+[[package]]
+name = "csv"
+version = "1.3.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "acdc4883a9c96732e4733212c01447ebd805833b7275a73ca3ee080fd77afdaf"
+dependencies = [
+ "csv-core",
+ "itoa",
+ "ryu",
+ "serde",
+]
+
+[[package]]
+name = "csv-core"
+version = "0.1.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7d02f3b0da4c6504f86e9cd789d8dbafab48c2321be74e9987593de5a894d93d"
+dependencies = [
+ "memchr",
+]
+
 [[package]]
 name = "darling"
 version = "0.20.10"
@@ -378,7 +402,7 @@ dependencies = [
 
 [[package]]
 name = "examples"
-version = "0.3.4"
+version = "0.4.1"
 dependencies = [
  "bcore",
  "ndarray 0.16.1",
@@ -1047,7 +1071,7 @@ dependencies = [
 
 [[package]]
 name = "python_wrap"
-version = "0.3.4"
+version = "0.4.1"
 dependencies = [
  "bcore",
  "numpy",
@@ -1217,18 +1241,18 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "serde"
-version = "1.0.216"
+version = "1.0.219"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "0b9781016e935a97e8beecf0c933758c97a5520d32930e460142b4cd80c6338e"
+checksum = "5f0e2c6ed6606019b4e29e69dbaba95b11854410e5347d525002456dbbb786b6"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.216"
+version = "1.0.219"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "46f859dbbf73865c6627ed570e78961cd3ac92407a2d117204c49232485da55e"
+checksum = "5b0276cf7f2c73365f7157c8123c21cd9a50fbbd844757af28ca1f5925fc2a00"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1237,9 +1261,9 @@ dependencies = [
 
 [[package]]
 name = "serde_json"
-version = "1.0.135"
+version = "1.0.140"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "2b0d7ba2887406110130a978386c4e1befb98c674b4fba677954e4db976630d9"
+checksum = "20068b6e96dc6c9bd23e01df8827e6c7e1f2fddd43c21810382803c136b99373"
 dependencies = [
  "itoa",
  "memchr",
diff --git a/Cargo.toml b/Cargo.toml
index c7b6872..75fd6a7 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -7,7 +7,7 @@ members = [
 resolver = "2"
 
 [workspace.package]
-version = "0.3.4"
+version = "0.4.1"
 edition = "2021"
 license = "MIT"
 repository = "https://github.com/Benncs/BioMC_PostProcess/"
diff --git a/core/Cargo.toml b/core/Cargo.toml
index 25632d7..540e0a0 100644
--- a/core/Cargo.toml
+++ b/core/Cargo.toml
@@ -12,8 +12,11 @@ authors.workspace = true
 publish = true
 
 [dependencies]
+csv = "1.3.1"
 hdf5 = "0.8.1"
 ndarray = "0.16.1"
+serde = { version = "1.0.219", features = ["derive"] }
+serde_json = "1.0.140"
 thiserror = "2.0.11"
 #hdf5-sys = { version = "0.8.1", features = ["static"] }
 
diff --git a/core/src/api.rs b/core/src/api.rs
index df2f396..fd33d17 100644
--- a/core/src/api.rs
+++ b/core/src/api.rs
@@ -1,8 +1,7 @@
-use crate::datamodel::Weight;
+use crate::datamodel::{Tallies, Weight};
 use crate::error::ApiError;
 use ndarray::{Array1, Array2, ArrayView3};
 
-
 /// `Phase` enum represents different states or phases of a substance.
 #[derive(Clone, PartialEq, Copy)]
 pub enum Phase {
@@ -10,14 +9,13 @@ pub enum Phase {
     Gas,
 }
 
-/// Type of estimator to retrieve data from MC Particle  
+/// Type of estimator to retrieve data from MC Particle
 #[derive(Copy, Clone)]
 pub enum Estimator {
     MonteCarlo,
     Weighted,
 }
 
-
 /// A trait for postprocessing operations on simulation results.
 ///
 /// This trait defines various methods for analyzing and retrieving data from simulation results.
@@ -30,6 +28,8 @@ pub trait PostProcessReader {
 
     fn weight(&self) -> &Weight;
 
+    fn tailles(&self) -> Option<&Tallies>;
+
     /// Returns a 1D array view of the time data from the simulation results.
     ///
     /// # Returns
@@ -173,15 +173,12 @@ pub trait PostProcessReader {
     fn get_population_mean(&self, key: &str, i_export: usize) -> Result<f64, ApiError>;
 }
 
-
-
 pub trait ModelEstimator {
     fn mu_direct(&self) -> Result<Array1<f64>, ApiError>;
 
     fn estimate(&self, etype: Estimator, key: &str, i_export: usize) -> Result<f64, ApiError>;
 
     fn estimate_time(&self, etype: Estimator, key: &str) -> Result<Array1<f64>, ApiError>;
-
 }
 
 #[cfg(test)]
@@ -194,8 +191,8 @@ mod tests {
         let rx = Array1::from(vec![2.0, 4.0, 6.0]);
         let weight = 2.0;
 
-
-        let result = crate::process::estimate(Estimator::MonteCarlo, &Weight::Single(weight), &rx).unwrap();
+        let result =
+            crate::process::estimate(Estimator::MonteCarlo, &Weight::Single(weight), &rx).unwrap();
         let dim = rx.dim();
         let weighted_estimator: f64 = (rx * weight).sum(); // (2.0*2.0 + 4.0*2.0 + 6.0*2.0) = 24.0
         let normalization_factor = (0..dim).map(|_| weight).sum::<f64>(); // 2.0 * 3 = 6.0
@@ -208,7 +205,8 @@ mod tests {
         let rx = Array1::from(vec![2.0, 4.0, 6.0]);
         let weight = 2.0;
 
-        let result = crate::process::estimate(Estimator::Weighted, &Weight::Single(weight), &rx).unwrap();
+        let result =
+            crate::process::estimate(Estimator::Weighted, &Weight::Single(weight), &rx).unwrap();
 
         let weighted_estimator: f64 = (rx * weight).sum(); // (2.0*2.0 + 4.0*2.0 + 6.0*2.0) = 24.0
         let expected_result = weighted_estimator; // Since it's weighted, it should return the weighted sum.
@@ -220,7 +218,8 @@ mod tests {
         let rx = Array1::from(vec![2.0, 4.0, 6.0]);
         let weight = 0.0;
 
-        let result = crate::process::estimate(Estimator::MonteCarlo, &Weight::Single(weight), &rx).unwrap();
+        let result =
+            crate::process::estimate(Estimator::MonteCarlo, &Weight::Single(weight), &rx).unwrap();
         assert_eq!(result, 0.0);
     }
 
@@ -228,7 +227,8 @@ mod tests {
     fn test_empty_array() {
         let rx = Array1::from(vec![]);
         let weight = 2.0;
-        let result = crate::process::estimate(Estimator::Weighted, &Weight::Single(weight), &rx).unwrap();
+        let result =
+            crate::process::estimate(Estimator::Weighted, &Weight::Single(weight), &rx).unwrap();
 
         // With an empty array, the result should be zero
         assert_eq!(result, 0.0);
diff --git a/core/src/datamodel/_impl.rs b/core/src/datamodel/_impl.rs
index dab9d92..9ba6e75 100644
--- a/core/src/datamodel/_impl.rs
+++ b/core/src/datamodel/_impl.rs
@@ -1,6 +1,6 @@
 use crate::process::Histogram;
 
-use super::main_file::{MainFInal, MainInitial, MainRecords, Misc};
+use super::main_file::{MainFInal, MainInitial, MainRecords, Misc, Tallies};
 use super::{Dim, ResultGroup};
 use hdf5::Group;
 use ndarray::{s, Array1, Array2, ArrayView1};
@@ -72,7 +72,7 @@ fn read_spatial_model_properties(
 
         // Access the "biological_model" group
         let group = file.group("biological_model")?;
-        //TODO: use group.len() instead of n_export 
+        //TODO: use group.len() instead of n_export
         for i_e in 0..n_export {
             // Read the data for the current export index
             let tmp: Vec<f64> = match group.dataset(&format!("{}/spatial/{}", i_e, key)) {
@@ -88,13 +88,13 @@ fn read_spatial_model_properties(
             if tmp_array.len() == slice_shape {
                 cx.slice_mut(s![i_e, ..])
                     .zip_mut_with(&tmp_array, |a, b| *a += b);
-                } else {
-                    eprintln!(
-                        "Shape mismatch: cx[{}, ..].shape = {}, tmp.shape = {}",
-                        i_e,
-                        slice_shape,
-                        tmp_array.len()
-                    );
+            } else {
+                eprintln!(
+                    "Shape mismatch: cx[{}, ..].shape = {}, tmp.shape = {}",
+                    i_e,
+                    slice_shape,
+                    tmp_array.len()
+                );
             }
         }
     }
@@ -115,10 +115,9 @@ pub fn read_model_properties(
         let group = file.group("biological_model")?;
         // Not all nodes have th=e same number of export so it happens that i_export is >
         // number_export for the current file
-        if (group.len() as usize)>=i_export{
+        if (group.len() as usize) >= i_export {
             let dataset = group.dataset(&format!("{}/{}", i_export, key))?;
             total_size += dataset.size();
-
         }
     }
 
@@ -130,14 +129,15 @@ pub fn read_model_properties(
 
         // Access the "biological_model" group
         let group = file.group("biological_model")?;
-        if (group.len() as usize)>=i_export{
+        if (group.len() as usize) >= i_export {
             let dataset = group.dataset(&format!("{}/{}", i_export, key))?;
 
             // Read the dataset into a temporary array
             let temp_array: Vec<f64> = dataset.read_raw::<f64>()?;
-            let tmp_array = ArrayView1::from_shape(temp_array.len(), &temp_array).map_err(|_| {
-                hdf5::Error::Internal("Shape mismatch while creating ArrayView1".to_string())
-            })?;
+            let tmp_array =
+                ArrayView1::from_shape(temp_array.len(), &temp_array).map_err(|_| {
+                    hdf5::Error::Internal("Shape mismatch while creating ArrayView1".to_string())
+                })?;
 
             // Copy the data into the result array
             result
@@ -151,27 +151,28 @@ pub fn read_model_properties(
     Ok(result)
 }
 
-pub fn get_n_export_real(files:&[String])->hdf5::Result<usize>
-{
-    if files.is_empty()
-    {
+pub fn get_n_export_real(files: &[String]) -> hdf5::Result<usize> {
+    if files.is_empty() {
         panic!("FIXME: not enough files")
     }
     let file = hdf5::File::open_as(&files[0], hdf5::file::OpenMode::Read)?;
     let group = file.group("biological_model")?;
     let group_size = group.len() as usize; //We export n_export times properties but if there is no
                                            //particle we do not export. group_size <= n_export and for
-    Ok(group_size) 
+    Ok(group_size)
 }
 
-
-pub fn make_histogram(files:&[String],i_export:usize,key:&str,hist:&mut Histogram)->hdf5::Result<()>
-{
+pub fn make_histogram(
+    files: &[String],
+    i_export: usize,
+    key: &str,
+    hist: &mut Histogram,
+) -> hdf5::Result<()> {
     for filename in files.iter() {
         // Open the HDF5 file in read mode
         let file = hdf5::File::open_as(filename, hdf5::file::OpenMode::Read)?;
         let group = file.group("biological_model")?;
-        if (group.len() as usize)>=i_export{
+        if (group.len() as usize) >= i_export {
             let dataset = group.dataset(&format!("{}/{}", i_export, key))?;
             let temp_array: Vec<f64> = dataset.read_raw::<f64>()?;
             hist.add(temp_array);
@@ -194,8 +195,8 @@ pub fn read_avg_model_properties(
         let group = file.group("biological_model")?;
         let group_size = group.len() as usize; //We export n_export times properties but if there is no
                                                //particle we do not export. group_size <= n_export and for
-                                               //all i > group_size , value is set to 0   
-        for i_e in 0..group_size{
+                                               //all i > group_size , value is set to 0
+        for i_e in 0..group_size {
             let dataset = group.dataset(&format!("{}/{}", i_e, key))?;
             let temp_array: Vec<f64> = dataset.read_raw::<f64>()?;
             result[i_e] += temp_array.iter().sum::<f64>();
@@ -252,12 +253,16 @@ impl ResultGroup<MainRecords> for Group {
             _ => (None, None),
         };
 
-        let mtr = match self.dataset("mtr") 
-        {
+        let mtr = match self.dataset("mtr") {
             Ok(_mtr) => Some(_mtr.read_raw::<f64>()?),
             _ => None,
         };
 
+        let tallies = match self.dataset("tallies") {
+            Ok(_t) => Some(Tallies(_t.read_raw::<f64>()?)),
+            _ => None,
+        };
+
         let shape = self.dataset("concentration_liquid")?.shape();
         let dim = Dim(shape[1], shape[2]);
         let time = read_vec!(self, "time", f64);
@@ -267,6 +272,7 @@ impl ResultGroup<MainRecords> for Group {
             concentration_gas,
             volume_gas,
             mtr,
+            tallies,
             dim,
             time,
         })
@@ -275,20 +281,25 @@ impl ResultGroup<MainRecords> for Group {
 
 impl ResultGroup<MainFInal> for Group {
     fn read_g(&self) -> hdf5::Result<MainFInal> {
-        let ds_events = self.group("events")?;
-        let mut events: HashMap<String, u64> = HashMap::new();
-        ds_events
-            .iter_visit_default(&mut events, |group, name, _link_info, fields| {
-                if let Ok(dataset) = group.dataset(name) {
-                    if let Ok(value) = dataset.read_scalar::<u64>() {
-                        fields.insert(name.to_string(), value);
-                    }
-                }
-                true
-            })
-        .unwrap();
         let number_particles = read_scalar!(self, "number_particles", u64);
 
+        let events = if let Ok(ds_events) = self.group("events") {
+            let mut events: HashMap<String, u64> = HashMap::new();
+            ds_events
+                .iter_visit_default(&mut events, |group, name, _link_info, fields| {
+                    if let Ok(dataset) = group.dataset(name) {
+                        if let Ok(value) = dataset.read_scalar::<u64>() {
+                            fields.insert(name.to_string(), value);
+                        }
+                    }
+                    true
+                })
+                .unwrap();
+            Some(events)
+        } else {
+            None
+        };
+
         Ok(MainFInal {
             events,
             number_particles,
diff --git a/core/src/datamodel/main_file.rs b/core/src/datamodel/main_file.rs
index c06da2f..01187b3 100644
--- a/core/src/datamodel/main_file.rs
+++ b/core/src/datamodel/main_file.rs
@@ -3,18 +3,59 @@
 //! Provides objects and methods to read the simulation's main file.
 //! The object hierarchy mimics the file's structure:
 
-
+use super::{Dim, ResultGroup, Weight};
+use csv::Writer;
+use serde::{Deserialize, Serialize};
+use serde_json;
 use std::collections::HashMap;
-use super::{Dim, ResultGroup,Weight};
-
-///File's mics section 
+///File's mics section
 #[derive(Debug)]
 pub struct Misc {
     pub n_node_thread: u64,
     pub n_rank: u64,
 }
 
-///Time dependent scalar records  
+#[derive(Debug, Serialize, Deserialize)]
+pub struct Tallies(pub Vec<f64>);
+
+impl Tallies {
+    pub fn validate(&self) -> bool {
+        self.0.len() % 6 == 0
+    }
+
+    pub fn to_json(&self) -> serde_json::Result<String> {
+        serde_json::to_string_pretty(&self.0)
+    }
+
+    pub fn to_csv(&self) -> Result<String, String> {
+        if !self.validate() {
+            return Err(
+                "Validation failed: The number of elements is not divisible by 6.".to_string(),
+            );
+        }
+
+        let headers = vec![
+            "NewParticle",
+            "Death",
+            "Move",
+            "Exit",
+            "Overflow",
+            "ChangeWeight",
+        ];
+        let mut wtr = Writer::from_writer(vec![]);
+
+        wtr.write_record(&headers).map_err(|e| e.to_string())?;
+
+        for row in self.0.chunks(6) {
+            wtr.serialize(row).map_err(|e| e.to_string())?;
+        }
+        let data = String::from_utf8(wtr.into_inner().map_err(|e| e.to_string())?)
+            .map_err(|e| e.to_string())?;
+        Ok(data)
+    }
+}
+
+///Time dependent scalar records
 #[derive(Debug)]
 pub struct MainRecords {
     pub concentration_liquid: Vec<f64>,
@@ -22,11 +63,12 @@ pub struct MainRecords {
     pub concentration_gas: Option<Vec<f64>>,
     pub volume_gas: Option<Vec<f64>>,
     pub mtr: Option<Vec<f64>>,
+    pub tallies: Option<Tallies>,
     pub dim: Dim,
-    pub time:Vec<f64>,
+    pub time: Vec<f64>,
 }
 
-///Initial information   
+///Initial information
 #[derive(Debug)]
 pub struct MainInitial {
     pub delta_time: f64,
@@ -39,21 +81,21 @@ pub struct MainInitial {
     pub t_per_flow_map: f64,
 }
 
-///Final information   
+///Final information
 #[derive(Debug)]
 pub struct MainFInal {
-    pub events: HashMap<String, u64>,
+    pub events: Option<HashMap<String, u64>>,
     pub number_particles: u64,
 }
 
-///Object that stores data main file     
+///Object that stores data main file
 #[derive(Debug)]
 pub struct MainResult {
     pub records: MainRecords,
     pub initial: MainInitial,
     pub cfinal: MainFInal,
     pub misc: Misc,
-    pub weight: Weight
+    pub weight: Weight,
 }
 
 impl MainResult {
@@ -65,14 +107,13 @@ impl MainResult {
 
         let m_ds = file.group("misc")?;
         let misc = ResultGroup::<Misc>::read_g(&m_ds)?;
-        
+
         let m_ds = file.group("records")?;
         let records = ResultGroup::<MainRecords>::read_g(&m_ds)?;
 
         let m_ds = file.group("final_result")?;
         let cfinal = ResultGroup::<MainFInal>::read_g(&m_ds)?;
 
-
         let weight = Weight::Single(initial.initial_weight); //TODO switch between single and multi weight
 
         Ok(MainResult {
@@ -80,12 +121,11 @@ impl MainResult {
             initial,
             cfinal,
             misc,
-            weight
+            weight,
         })
     }
 
-    pub fn time(&self)->&[f64]
-    {
+    pub fn time(&self) -> &[f64] {
         &self.records.time
     }
-}
\ No newline at end of file
+}
diff --git a/core/src/datamodel/mod.rs b/core/src/datamodel/mod.rs
index 2a3a50e..447cea5 100644
--- a/core/src/datamodel/mod.rs
+++ b/core/src/datamodel/mod.rs
@@ -5,7 +5,7 @@ pub use _impl::{
     get_n_export_real, make_histogram, read_avg_model_properties, read_model_mass,
     read_model_properties,
 };
-pub use main_file::MainResult;
+pub use main_file::{MainResult, Tallies};
 use ndarray::{Array2, ArrayView2, ArrayView3};
 use std::path::PathBuf;
 
@@ -93,7 +93,7 @@ pub fn vec_to_array_view2(vec: &[f64], nr: usize, nc: usize) -> ArrayView2<'_, f
     ArrayView2::from_shape((nr, nc), vec).expect("Failed to create ArrayView2")
 }
 
-pub fn vec_to_array_view3<'a>(vec: &'a [f64], dim: &'a Dim, nt: usize) -> ArrayView3<'a,f64> {
+pub fn vec_to_array_view3<'a>(vec: &'a [f64], dim: &'a Dim, nt: usize) -> ArrayView3<'a, f64> {
     assert_eq!(
         vec.len(),
         nt * dim.0 * dim.1,
diff --git a/core/src/impl_concat.rs b/core/src/impl_concat.rs
index 8bfd0ad..30e57e3 100644
--- a/core/src/impl_concat.rs
+++ b/core/src/impl_concat.rs
@@ -1,6 +1,6 @@
 use crate::api::PostProcessReader;
-use crate::datamodel::Weight;
-use crate::{error::ApiError, api::Phase, PostProcess};
+use crate::datamodel::{Tallies, Weight};
+use crate::{api::Phase, error::ApiError, PostProcess};
 use ndarray::{Array1, Array2, ArrayView3, Axis};
 
 #[derive(Debug)]
@@ -196,4 +196,7 @@ impl PostProcessReader for ConcatPostPrcess {
     fn get_population_mean(&self, key: &str, i_export: usize) -> Result<f64, ApiError> {
         todo!()
     }
+    fn tailles(&self) -> Option<&Tallies> {
+        todo!()
+    }
 }
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index 3789414..d9cf392 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -1,7 +1,7 @@
 use crate::api::{ModelEstimator, PostProcessReader};
 use crate::datamodel::{
     get_n_export_real, read_avg_model_properties, read_model_mass, read_model_properties,
-    vec_to_array_view2, vec_to_array_view3, Dim, Weight,
+    vec_to_array_view2, vec_to_array_view3, Dim, Tallies, Weight,
 };
 use crate::datamodel::{make_histogram, Results};
 use crate::process::{spatial_average_concentration, Histogram};
@@ -339,6 +339,9 @@ impl PostProcessReader for PostProcess {
             Err(e) => Err(ApiError::Io(e)),
         }
     }
+    fn tailles(&self) -> Option<&Tallies> {
+        self.results.main.records.tallies.as_ref()
+    }
 }
 
 impl ModelEstimator for PostProcess {
diff --git a/examples/example_rust.rs b/examples/example_rust.rs
index b11e531..e95c8c0 100644
--- a/examples/example_rust.rs
+++ b/examples/example_rust.rs
@@ -1,14 +1,12 @@
-use bcore::{PostProcess,PostProcessReader};
+use bcore::{PostProcess, PostProcessReader};
 use ndarray::s;
 use plotly::ImageFormat;
 use plotly::{Layout, Plot, Scatter};
 fn main() {
     if let Ok(obj) = PostProcess::new(
-        "cstr_0",
-        Some("/home-local/casale/Documents/thesis/simulations/ecoli_model_2024/out/steady_1/".to_string()),
+        "str_1",
+        Some("/home-local/casale/Documents/thesis/simulations/meta/out_str_nu_redis_2".to_string()),
     ) {
-       
-
         let x = obj.get_biomass_concentration().unwrap();
         let time: Vec<f64> = obj.time().into_iter().map(|t| t / 3600.).collect();
         let xvec = x.slice(s![.., 0]).to_vec();
@@ -31,9 +29,13 @@ fn main() {
         plot.write_image("./examples/out.svg", ImageFormat::SVG, 800, 600, 1.0);
         plot.write_html("./examples/out.html");
 
-        println!("{}",plot.to_inline_html(Some("div_plot_x")));
-    }
-    else {
+        println!("{}", plot.to_inline_html(Some("div_plot_x")));
+
+        println!(
+            "{}",
+            obj.tailles().expect("REASON").to_csv().expect("REASE")
+        );
+    } else {
         println!("Simulation not found");
     }
 }
diff --git a/examples/out.html b/examples/out.html
index 711865b..e54b4c9 100644
--- a/examples/out.html
+++ b/examples/out.html
@@ -16,7 +16,7 @@
 
         <script type="module">
             const graph_div = document.getElementById("plotly-html-element");
-            await Plotly.newPlot(graph_div, {"data":[{"type":"scatter","name":"Biomass Concentration","mode":"lines","x":[0.0,0.9694444444444444,1.9394444444444445,2.9094444444444445,3.8794444444444443,4.849444444444444,5.819444444444445,6.789444444444444,7.759444444444444,8.729444444444445,9.699444444444444,10.669444444444444,11.639444444444445,12.609444444444444,13.579444444444444,14.549444444444445,15.519444444444444,16.489444444444445,17.459444444444443,18.429444444444446,19.399444444444445,20.369444444444444,21.339444444444446,22.309444444444445,23.279444444444444,24.249444444444446,25.219444444444445,26.189444444444444,27.159444444444443,28.129444444444445,29.099444444444444,30.069444444444443,31.039444444444445,32.00944444444445,32.97944444444445,33.949444444444445,34.919444444444444,35.88944444444444,36.85944444444444,37.82944444444445,38.79944444444445,39.769444444444446,40.739444444444445,41.70944444444444,42.67944444444444,43.64944444444444,44.61944444444445,45.589444444444446,46.559444444444445,47.529444444444444,48.49944444444444,49.46944444444444,50.43944444444445,51.409444444444446,52.379444444444445,53.349444444444444,54.31944444444444,55.28944444444444,56.25944444444445,57.22944444444445,58.199444444444445,59.169444444444444,60.13944444444444,61.10944444444444,62.07944444444445,63.04944444444445,64.01944444444445,64.98944444444444,65.95944444444444,66.92944444444444,67.89944444444444,68.86944444444444,69.83944444444444,70.80944444444444,71.77944444444445,72.74944444444445,73.71944444444445,74.68944444444445,75.65944444444445,76.62944444444445,77.59944444444444,78.56944444444444,79.53944444444444,80.50944444444444,81.47944444444444,82.44944444444444,83.41944444444445,84.38944444444445,85.35944444444445,86.32944444444445,87.29944444444445,88.26944444444445,89.23944444444444,90.20944444444444,91.17944444444444,92.14944444444444,93.11944444444444,94.08944444444444,95.05944444444444,96.00055555555555],"y":[1.0,1.4604036396633084,2.2496771390447097,3.0340278779370453,2.9995666464389688,2.9655959017986775,2.9372270635433573,2.9008311393645374,2.8779681888436666,2.846184536710327,2.8265516596614115,2.803897734327263,2.7837851433732737,2.7688085877174005,2.753498436466982,2.7367914740777857,2.7085335984938186,2.690115916238367,2.675321450965318,2.66367104624251,2.647807862616911,2.6398982735197745,2.6168051458642405,2.597168451848322,2.5835944262025556,2.574823601909119,2.559903817420286,2.5501392110695704,2.5348875494413714,2.522725958145144,2.5092300590452266,2.492572693770458,2.489272501000557,2.4843703484117334,2.4794095813794192,2.468706247705731,2.46590588957613,2.4538890721643103,2.4501222264959392,2.4455331510807325,2.439760227469058,2.430724962428687,2.4319804894926764,2.4252216810886975,2.4222859487602633,2.4089860016625892,2.4040830154898996,2.4009248400648584,2.392600932433475,2.391373609132103,2.3851021306682236,2.3732590921491323,2.3655253619784626,2.3621974425660524,2.3588308885862954,2.3532353194748845,2.357728140197613,2.3551657515730007,2.3479532491147883,2.351270310210964,2.3351046396515214,2.3256807270755835,2.320495874078731,2.3244490928486874,2.3251520138763704,2.326801682768065,2.325982347531971,2.3223526010225664,2.314528181576889,2.3030144915069273,2.299049374129489,2.2865382424837186,2.287312094335708,2.2764902417855923,2.281859228001982,2.2824728215796553,2.280625756360304,2.280415573968347,2.2766508043499156,2.276356492185855,2.289471904229777,2.2905574943899456,2.2896466935949302,2.2864744758011555,2.282296951599325,2.2806129748526347,2.2738352521536447,2.281564335629175,2.2920214589112784,2.287682474226786,2.286864485170161,2.290782107147607,2.2922425047122816,2.2938552340220673,2.294034933425964,2.297716759680781,2.295829110381153,2.2968285733137392,2.2880273309814525,2.28793524008686],"line":{"width":2.0,"color":"red"}}],"layout":{"title":{"text":"Biomass Concentration Over Time"},"xaxis":{"title":{"text":"Time (h)"}},"yaxis":{"title":{"text":"Biomass Concentration (g/L)"}}},"config":{}});
+            await Plotly.newPlot(graph_div, {"data":[{"type":"scatter","name":"Biomass Concentration","mode":"lines","x":[3.000002777830366,3.6122250000525886,4.2245861111637,4.83694722227481,5.449308333385922,6.061669444497033,6.6740305556081445,7.286391666719255,7.898752777830366,8.511113888941477,9.123475000052588,9.7358361111637,10.348197222274809,10.96055833338592,11.572919444497032,12.185280555608143,12.797641666719255,13.410002777830366,14.022363888941477,14.634725000052587,15.247086111163698,15.85944722227481,16.471808333385923,17.084169444497032,17.696530555608142,18.308891666719255,18.921252777830365,19.533613888941478,20.145975000052587,20.7583361111637,21.37069722227481,21.98305833338592,22.595419444497033,23.207780555608142,23.820141666719255,24.432502777830365,25.044863888941478,25.657225000052588,26.269586111163697,26.88194722227481,27.49430833338592,28.106669444497033,28.719030555608143,29.331391666719256,29.943752777830365,30.556113888941475,31.168475000052588,31.780836111163698,32.39319722227481,33.00014166671925],"y":[2.036127910519303,2.139208228127089,2.144343260163567,2.1492561217830066,2.1542373332287807,2.160100365208958,2.165157046714609,2.169920993741122,2.1732528534581665,2.176840476547387,2.1810530133044934,2.1845265146485113,2.1862610162454397,2.189226619427489,2.191510998057437,2.194537414291351,2.1967929200858562,2.1979657951908464,2.1997096989724634,2.202436136536434,2.204365830200866,2.2037222168250277,2.2069298800519044,2.2081872153294633,2.2089545899358516,2.2140269020167405,2.216376972589069,2.2179805677660283,2.219271742565363,2.2217410506247264,2.2218895241907717,2.2220544759468526,2.22268144307836,2.222546495883065,2.223310995326347,2.224291451851895,2.2248080413451823,2.224585179088409,2.224466558265803,2.2247957956407687,2.2255440018217563,2.2275808453037427,2.228333595669837,2.2296815547418998,2.229973468599975,2.2317201641217843,2.2330961849454902,2.233854834229117,2.2340413727001462,2.234817209909141],"line":{"width":2.0,"color":"red"}}],"layout":{"title":{"text":"Biomass Concentration Over Time"},"xaxis":{"title":{"text":"Time (h)"}},"yaxis":{"title":{"text":"Biomass Concentration (g/L)"}}},"config":{}});
         </script>
     </div>
 </body>
diff --git a/examples/out.svg b/examples/out.svg
index 6b75874..c5b0d47 100644
--- a/examples/out.svg
+++ b/examples/out.svg
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file

From 563670b208f1518be9ccc7d132935f82e882f827 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Thu, 3 Apr 2025 15:15:11 +0200
Subject: [PATCH 02/14] feat(tallies): conversion from tallies to Array2View
 and to Numpy

---
 core/src/api.rs                 |  5 ++--
 core/src/datamodel/_impl.rs     |  3 +-
 core/src/datamodel/main_file.rs | 44 ++---------------------------
 core/src/datamodel/mod.rs       |  3 +-
 core/src/datamodel/tallies.rs   | 49 +++++++++++++++++++++++++++++++++
 core/src/impl_concat.rs         |  5 ++--
 core/src/impl_unique.rs         |  4 +--
 examples/example_rust.rs        |  2 +-
 python_wrap/src/lib.rs          | 19 +++++++++++++
 9 files changed, 83 insertions(+), 51 deletions(-)
 create mode 100644 core/src/datamodel/tallies.rs

diff --git a/core/src/api.rs b/core/src/api.rs
index fd33d17..dff612d 100644
--- a/core/src/api.rs
+++ b/core/src/api.rs
@@ -1,4 +1,5 @@
-use crate::datamodel::{Tallies, Weight};
+use crate::datamodel::{Weight,tallies::Tallies};
+
 use crate::error::ApiError;
 use ndarray::{Array1, Array2, ArrayView3};
 
@@ -28,7 +29,7 @@ pub trait PostProcessReader {
 
     fn weight(&self) -> &Weight;
 
-    fn tailles(&self) -> Option<&Tallies>;
+    fn tallies(&self) -> Option<&Tallies>;
 
     /// Returns a 1D array view of the time data from the simulation results.
     ///
diff --git a/core/src/datamodel/_impl.rs b/core/src/datamodel/_impl.rs
index 9ba6e75..5b45264 100644
--- a/core/src/datamodel/_impl.rs
+++ b/core/src/datamodel/_impl.rs
@@ -1,6 +1,7 @@
 use crate::process::Histogram;
 
-use super::main_file::{MainFInal, MainInitial, MainRecords, Misc, Tallies};
+use super::main_file::{MainFInal, MainInitial, MainRecords, Misc};
+use super::tallies::Tallies;
 use super::{Dim, ResultGroup};
 use hdf5::Group;
 use ndarray::{s, Array1, Array2, ArrayView1};
diff --git a/core/src/datamodel/main_file.rs b/core/src/datamodel/main_file.rs
index 01187b3..57217ab 100644
--- a/core/src/datamodel/main_file.rs
+++ b/core/src/datamodel/main_file.rs
@@ -3,11 +3,9 @@
 //! Provides objects and methods to read the simulation's main file.
 //! The object hierarchy mimics the file's structure:
 
-use super::{Dim, ResultGroup, Weight};
-use csv::Writer;
-use serde::{Deserialize, Serialize};
-use serde_json;
+use super::{tallies::Tallies, Dim, ResultGroup, Weight};
 use std::collections::HashMap;
+use ndarray::{ArrayView2};
 ///File's mics section
 #[derive(Debug)]
 pub struct Misc {
@@ -15,45 +13,7 @@ pub struct Misc {
     pub n_rank: u64,
 }
 
-#[derive(Debug, Serialize, Deserialize)]
-pub struct Tallies(pub Vec<f64>);
 
-impl Tallies {
-    pub fn validate(&self) -> bool {
-        self.0.len() % 6 == 0
-    }
-
-    pub fn to_json(&self) -> serde_json::Result<String> {
-        serde_json::to_string_pretty(&self.0)
-    }
-
-    pub fn to_csv(&self) -> Result<String, String> {
-        if !self.validate() {
-            return Err(
-                "Validation failed: The number of elements is not divisible by 6.".to_string(),
-            );
-        }
-
-        let headers = vec![
-            "NewParticle",
-            "Death",
-            "Move",
-            "Exit",
-            "Overflow",
-            "ChangeWeight",
-        ];
-        let mut wtr = Writer::from_writer(vec![]);
-
-        wtr.write_record(&headers).map_err(|e| e.to_string())?;
-
-        for row in self.0.chunks(6) {
-            wtr.serialize(row).map_err(|e| e.to_string())?;
-        }
-        let data = String::from_utf8(wtr.into_inner().map_err(|e| e.to_string())?)
-            .map_err(|e| e.to_string())?;
-        Ok(data)
-    }
-}
 
 ///Time dependent scalar records
 #[derive(Debug)]
diff --git a/core/src/datamodel/mod.rs b/core/src/datamodel/mod.rs
index 447cea5..739a861 100644
--- a/core/src/datamodel/mod.rs
+++ b/core/src/datamodel/mod.rs
@@ -1,11 +1,12 @@
 mod _impl;
 mod main_file;
+pub mod tallies;
 use crate::error::ApiError;
 pub use _impl::{
     get_n_export_real, make_histogram, read_avg_model_properties, read_model_mass,
     read_model_properties,
 };
-pub use main_file::{MainResult, Tallies};
+pub use main_file::MainResult;
 use ndarray::{Array2, ArrayView2, ArrayView3};
 use std::path::PathBuf;
 
diff --git a/core/src/datamodel/tallies.rs b/core/src/datamodel/tallies.rs
new file mode 100644
index 0000000..694595b
--- /dev/null
+++ b/core/src/datamodel/tallies.rs
@@ -0,0 +1,49 @@
+use csv::Writer;
+use ndarray::ArrayView2;
+use serde::{Deserialize, Serialize};
+use serde_json;
+use super::vec_to_array_view2;
+#[derive(Debug, Serialize, Deserialize)]
+pub struct Tallies(pub Vec<f64>);
+
+impl Tallies {
+    pub fn validate(&self) -> bool {
+        self.0.len() % 6 == 0
+    }
+
+    pub fn to_json(&self) -> serde_json::Result<String> {
+        serde_json::to_string_pretty(&self.0)
+    }
+
+    pub fn to_csv(&self) -> Result<String, String> {
+        if !self.validate() {
+            return Err(
+                "Validation failed: The number of elements is not divisible by 6.".to_string(),
+            );
+        }
+
+        let headers = vec![
+            "NewParticle",
+            "Death",
+            "Move",
+            "Exit",
+            "Overflow",
+            "ChangeWeight",
+        ];
+        let mut wtr = Writer::from_writer(vec![]);
+
+        wtr.write_record(&headers).map_err(|e| e.to_string())?;
+
+        for row in self.0.chunks(6) {
+            wtr.serialize(row).map_err(|e| e.to_string())?;
+        }
+        let data = String::from_utf8(wtr.into_inner().map_err(|e| e.to_string())?)
+            .map_err(|e| e.to_string())?;
+        Ok(data)
+    }
+
+    pub fn to_array(&self)->ArrayView2<f64>
+    {
+        vec_to_array_view2(&self.0, self.0.len()/6, 6)
+    }
+}
\ No newline at end of file
diff --git a/core/src/impl_concat.rs b/core/src/impl_concat.rs
index 30e57e3..bf97748 100644
--- a/core/src/impl_concat.rs
+++ b/core/src/impl_concat.rs
@@ -1,5 +1,6 @@
 use crate::api::PostProcessReader;
-use crate::datamodel::{Tallies, Weight};
+use crate::datamodel::{Weight,tallies::Tallies};
+
 use crate::{api::Phase, error::ApiError, PostProcess};
 use ndarray::{Array1, Array2, ArrayView3, Axis};
 
@@ -196,7 +197,7 @@ impl PostProcessReader for ConcatPostPrcess {
     fn get_population_mean(&self, key: &str, i_export: usize) -> Result<f64, ApiError> {
         todo!()
     }
-    fn tailles(&self) -> Option<&Tallies> {
+    fn tallies(&self) -> Option<&Tallies> {
         todo!()
     }
 }
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index d9cf392..22f03d3 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -1,7 +1,7 @@
 use crate::api::{ModelEstimator, PostProcessReader};
 use crate::datamodel::{
     get_n_export_real, read_avg_model_properties, read_model_mass, read_model_properties,
-    vec_to_array_view2, vec_to_array_view3, Dim, Tallies, Weight,
+    vec_to_array_view2, vec_to_array_view3, Dim, tallies::Tallies, Weight,
 };
 use crate::datamodel::{make_histogram, Results};
 use crate::process::{spatial_average_concentration, Histogram};
@@ -339,7 +339,7 @@ impl PostProcessReader for PostProcess {
             Err(e) => Err(ApiError::Io(e)),
         }
     }
-    fn tailles(&self) -> Option<&Tallies> {
+    fn tallies(&self) -> Option<&Tallies> {
         self.results.main.records.tallies.as_ref()
     }
 }
diff --git a/examples/example_rust.rs b/examples/example_rust.rs
index e95c8c0..b4ac290 100644
--- a/examples/example_rust.rs
+++ b/examples/example_rust.rs
@@ -33,7 +33,7 @@ fn main() {
 
         println!(
             "{}",
-            obj.tailles().expect("REASON").to_csv().expect("REASE")
+            obj.tallies().expect("REASON").to_csv().expect("REASE")
         );
     } else {
         println!("Simulation not found");
diff --git a/python_wrap/src/lib.rs b/python_wrap/src/lib.rs
index f0ef0d1..b9e6501 100644
--- a/python_wrap/src/lib.rs
+++ b/python_wrap/src/lib.rs
@@ -329,6 +329,25 @@ impl PythonPostProcess {
             Err(e) => Err(PyErr::new::<PyRuntimeError, _>(e.to_string())),
         }
     }
+
+    pub fn get_csv_tallies(&self, py: Python<'_>)->PyResult<String>
+    {
+        match self.inner.tallies() {
+            Some(e) => Ok(e.to_csv().unwrap()),
+            None=> Err(PyErr::new::<PyRuntimeError, _>("No data")),
+        }
+    }
+
+    fn get_tallies(&self, py: Python<'_>) -> Py<PyArray2<f64>> {
+        match self.inner.tallies() {
+            Some(e) => 
+            {
+                let v = e.to_array().to_owned();
+                PyArray2::from_owned_array(py, v).unbind()
+            }
+            None => panic!("No data"),
+        }
+    }
 }
 
 #[pymodule]

From 2ae406a82b1a26bcea03b5f4a75ac04f7933b269 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Fri, 2 May 2025 13:17:13 +0200
Subject: [PATCH 03/14] feat: add spatial property getter and probe read

---
 Cargo.lock                      |  6 ++---
 Cargo.toml                      |  2 +-
 biomc_pp/rtd.py                 | 39 +++++++++++++++++++++++++++
 core/src/api.rs                 |  5 ++++
 core/src/datamodel/_impl.rs     | 20 +++++++++++++-
 core/src/datamodel/main_file.rs |  9 ++++---
 core/src/datamodel/mod.rs       | 47 ++++++++++++++++++++++++++++++---
 core/src/impl_concat.rs         | 10 +++++++
 core/src/impl_unique.rs         | 31 +++++++++++++++++++++-
 examples/out_hist.html          |  2 +-
 examples/out_hist.svg           |  2 +-
 pyproject.toml                  |  2 +-
 python_wrap/src/lib.rs          | 32 +++++++++++++++-------
 13 files changed, 183 insertions(+), 24 deletions(-)
 create mode 100644 biomc_pp/rtd.py

diff --git a/Cargo.lock b/Cargo.lock
index c2c54f4..5a57654 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -81,7 +81,7 @@ dependencies = [
 
 [[package]]
 name = "bcore"
-version = "0.4.1"
+version = "0.4.2"
 dependencies = [
  "csv",
  "hdf5",
@@ -402,7 +402,7 @@ dependencies = [
 
 [[package]]
 name = "examples"
-version = "0.4.1"
+version = "0.4.2"
 dependencies = [
  "bcore",
  "ndarray 0.16.1",
@@ -1071,7 +1071,7 @@ dependencies = [
 
 [[package]]
 name = "python_wrap"
-version = "0.4.1"
+version = "0.4.2"
 dependencies = [
  "bcore",
  "numpy",
diff --git a/Cargo.toml b/Cargo.toml
index 75fd6a7..08b55f6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -7,7 +7,7 @@ members = [
 resolver = "2"
 
 [workspace.package]
-version = "0.4.1"
+version = "0.4.2"
 edition = "2021"
 license = "MIT"
 repository = "https://github.com/Benncs/BioMC_PostProcess/"
diff --git a/biomc_pp/rtd.py b/biomc_pp/rtd.py
new file mode 100644
index 0000000..1750f47
--- /dev/null
+++ b/biomc_pp/rtd.py
@@ -0,0 +1,39 @@
+import biomc_pp 
+import numpy as np 
+import matplotlib.pyplot as plt 
+
+def get_rtd_from_scalar(pp,time,step_concentration):
+
+    c = pp.get_spatial_average_concentration(0,biomc_pp.Phase.Liquid)
+    c0 = c[0]
+    delta_c = c - c0
+    step_concentration = 5
+
+    # Cumulative probability 
+    f_rtd = delta_c / step_concentration  
+    # By defintion F(t)=integral 0 to t (E(t))
+    e_rtd = np.diff(f_rtd) / np.diff(time)
+
+    return f_rtd,e_rtd
+
+def get_rtd_particle(pp):
+    probes = pp.get_probes()/3600
+    return np.histogram(probes, bins=100,density=True)
+
+def plot_rtd(pp,time,step_concentration):
+    
+    f_rtd,e_rtd = get_rtd_from_scalar(pp,time,step_concentration)
+    plt.figure()
+    plt.plot(time[1:],e_rtd,'--',color='red',label='Scalar')
+    c,e = get_rtd_particle(pp)
+    plt.bar(
+        e[:-1],
+        c,
+        width=np.diff(e),
+        edgecolor="black",
+        alpha=0.7,
+        color="blue",
+        label="Particles"
+    )
+    return f_rtd,e_rtd
+
diff --git a/core/src/api.rs b/core/src/api.rs
index dff612d..6cbe99e 100644
--- a/core/src/api.rs
+++ b/core/src/api.rs
@@ -66,6 +66,8 @@ pub trait PostProcessReader {
     /// * `Array1<f64>` - A 1D array containing the spatial average concentrations over time.
     fn get_spatial_average_concentration(&self, species: usize, phase: Phase) -> Array1<f64>;
 
+    fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>;
+
     fn get_spatial_average_biomass_concentration(&self) -> Result<Array1<f64>, ApiError>;
 
     fn get_concentrations(&self, phase: Phase) -> ArrayView3<f64>;
@@ -96,6 +98,9 @@ pub trait PostProcessReader {
     ///   or an error message if the calculation fails.
     fn get_biomass_concentration(&self) -> Result<Array2<f64>, ApiError>;
 
+    fn get_probes(&self) -> Result<Array1<f64>, ApiError>;
+    
+
     /// Calculates the total growth in number.
     ///
     /// # Returns
diff --git a/core/src/datamodel/_impl.rs b/core/src/datamodel/_impl.rs
index 5b45264..25f1217 100644
--- a/core/src/datamodel/_impl.rs
+++ b/core/src/datamodel/_impl.rs
@@ -1,3 +1,4 @@
+use crate::error::ApiError;
 use crate::process::Histogram;
 
 use super::main_file::{MainFInal, MainInitial, MainRecords, Misc};
@@ -61,7 +62,7 @@ pub fn read_number_particle(filename: &str) -> hdf5::Result<Vec<f64>> {
     Ok(v)
 }
 
-fn read_spatial_model_properties(
+pub fn read_spatial_model_properties(
     key: &str,
     files: &[String],
     cx: &mut Array2<f64>,
@@ -102,6 +103,23 @@ fn read_spatial_model_properties(
     Ok(())
 }
 
+pub fn get_probe_size(files: &[String])-> Result<usize,ApiError>
+{
+    let mut probe_size = 0;
+    for filename in files.iter() {
+        let file = hdf5::File::open_as(filename, hdf5::file::OpenMode::Read)?;
+        if let Ok(dataset) = file.dataset("probes")
+        {
+            probe_size += dataset.size();
+        }
+        else {
+            return Err(ApiError::Default("No Probes in dataset".to_string()));
+        }
+        
+    }
+    Ok(probe_size)
+}
+
 pub fn read_model_properties(
     key: &str,
     files: &[String],
diff --git a/core/src/datamodel/main_file.rs b/core/src/datamodel/main_file.rs
index 57217ab..8714582 100644
--- a/core/src/datamodel/main_file.rs
+++ b/core/src/datamodel/main_file.rs
@@ -53,7 +53,7 @@ pub struct MainFInal {
 pub struct MainResult {
     pub records: MainRecords,
     pub initial: MainInitial,
-    pub cfinal: MainFInal,
+    pub cfinal: Option<MainFInal>, //TODO Add runtime parameter to throw error or not when missing
     pub misc: Misc,
     pub weight: Weight,
 }
@@ -71,8 +71,11 @@ impl MainResult {
         let m_ds = file.group("records")?;
         let records = ResultGroup::<MainRecords>::read_g(&m_ds)?;
 
-        let m_ds = file.group("final_result")?;
-        let cfinal = ResultGroup::<MainFInal>::read_g(&m_ds)?;
+        let mut cfinal = None;
+        if let Ok(m_ds) = file.group("final_result")
+        {
+            cfinal= Some(ResultGroup::<MainFInal>::read_g(&m_ds)?);
+        }
 
         let weight = Weight::Single(initial.initial_weight); //TODO switch between single and multi weight
 
diff --git a/core/src/datamodel/mod.rs b/core/src/datamodel/mod.rs
index 739a861..8e892e4 100644
--- a/core/src/datamodel/mod.rs
+++ b/core/src/datamodel/mod.rs
@@ -2,12 +2,13 @@ mod _impl;
 mod main_file;
 pub mod tallies;
 use crate::error::ApiError;
+use _impl::get_probe_size;
 pub use _impl::{
     get_n_export_real, make_histogram, read_avg_model_properties, read_model_mass,
-    read_model_properties,
+    read_model_properties, read_spatial_model_properties,
 };
 pub use main_file::MainResult;
-use ndarray::{Array2, ArrayView2, ArrayView3};
+use ndarray::{s, Array1, Array2, ArrayView1, ArrayView2, ArrayView3};
 use std::path::PathBuf;
 
 trait ResultGroup<T> {
@@ -81,7 +82,7 @@ impl Results {
                 // .collect();
             }
         }
-        todo!()
+        vec![] //Let say is normal behaviour to return empty vector if there is no properties instead
     }
 
     pub fn get_files(&self) -> &[String] {
@@ -89,6 +90,46 @@ impl Results {
     }
 }
 
+pub fn f_get_probes(files: &[String]) -> Result<Array1<f64>, ApiError> {
+    let total_size = get_probe_size(files)?;
+    let mut probe = Array1::zeros(total_size);
+    let mut offset = 0;
+
+    for filename in files.iter() {
+        let file = hdf5::File::open(filename)?;
+        // if let Ok(dataset) = file.dataset("probes") {
+        //     let temp_array: Vec<f64> = match dataset.read_raw::<f64>() {
+        //         Ok(data) => data,
+        //         Err(_) => return None,
+        //     };
+
+        //     let tmp_array = match ArrayView1::from_shape(temp_array.len(), &temp_array) {
+        //         Ok(view) => view,
+        //         Err(_) => return None,
+        //     };
+
+        //     probe
+        //         .slice_mut(s![offset..offset + temp_array.len()])
+        //         .assign(&tmp_array);
+        //     offset += temp_array.len();
+        // } else {
+        //     return None;
+        // }
+        let dataset = file.dataset("probes")?;
+        let temp_array: Vec<f64> = dataset.read_raw::<f64>()?;
+        let tmp_array = match ArrayView1::from_shape(temp_array.len(), &temp_array) {
+            Ok(view) => view,
+            Err(_) => return Err(ApiError::ShapeError),
+        };
+        probe
+            .slice_mut(s![offset..offset + temp_array.len()])
+            .assign(&tmp_array);
+        offset += temp_array.len();
+    }
+
+    Ok(probe)
+}
+
 pub fn vec_to_array_view2(vec: &[f64], nr: usize, nc: usize) -> ArrayView2<'_, f64> {
     assert_eq!(vec.len(), nr * nc, "Vector size must match dimensions.");
     ArrayView2::from_shape((nr, nc), vec).expect("Failed to create ArrayView2")
diff --git a/core/src/impl_concat.rs b/core/src/impl_concat.rs
index bf97748..a0e8fa7 100644
--- a/core/src/impl_concat.rs
+++ b/core/src/impl_concat.rs
@@ -47,6 +47,11 @@ impl PostProcessReader for ConcatPostPrcess {
         todo!()
     }
 
+    fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>
+    {
+        todo!()
+    }
+
     fn get_concentrations(&self, phase: Phase) -> ArrayView3<f64> {
         todo!()
     }
@@ -64,6 +69,11 @@ impl PostProcessReader for ConcatPostPrcess {
         Ok(concatenated)
     }
 
+    fn get_probes(&self) -> Result<Array1<f64>, ApiError>
+    {
+        todo!();
+    }
+
     fn get_property_names(&self) -> Vec<String> {
         self.dataset[0].get_property_names() //Names SHOULD be the same
     }
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index 22f03d3..9edeca3 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -3,7 +3,7 @@ use crate::datamodel::{
     get_n_export_real, read_avg_model_properties, read_model_mass, read_model_properties,
     vec_to_array_view2, vec_to_array_view3, Dim, tallies::Tallies, Weight,
 };
-use crate::datamodel::{make_histogram, Results};
+use crate::datamodel::{f_get_probes, make_histogram, read_spatial_model_properties, Results};
 use crate::process::{spatial_average_concentration, Histogram};
 use crate::{api::Estimator, api::Phase, error::ApiError};
 use ndarray::{s, Array1, Array2, ArrayView3, Axis};
@@ -193,6 +193,35 @@ impl PostProcessReader for PostProcess {
         }
     }
 
+    fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>
+    {
+        let nt: usize = self.results.main.records.time.len(); // Number of time steps
+        let num_dimensions = self.results.main.records.dim.0; // Dimensionality
+
+        // Initialize the biomass matrix
+        let mut biomass_matrix = Array2::zeros((nt, num_dimensions));
+
+        if !self.results.property_name.iter().any(|x| x == key) {
+            return Err(ApiError::KeyError(key.to_string()));
+        }
+
+        // Attempt to read model mass
+        if let Err(err) = read_spatial_model_properties(key,self.results.get_files(), &mut biomass_matrix, nt) {
+            return Err(ApiError::Io(err));
+        }
+
+
+        // Calculate biomass concentration
+        biomass_matrix /= self.get_number_particle();
+
+        Ok(biomass_matrix)
+    }
+
+    fn get_probes(&self) -> Result<Array1<f64>, ApiError>
+    {
+        f_get_probes(&self.results.files)
+    }
+
     /// Calculates the biomass concentration over time for the simulation.
     ///
     /// # Returns
diff --git a/examples/out_hist.html b/examples/out_hist.html
index 8c49c3b..595474a 100644
--- a/examples/out_hist.html
+++ b/examples/out_hist.html
@@ -16,7 +16,7 @@
 
         <script type="module">
             const graph_div = document.getElementById("plotly-html-element");
-            await Plotly.newPlot(graph_div, 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(nu_meta)","marker":{"color":"black"}}],"layout":{"title":{"text":"Final \\nu_{eff}"},"showlegend":true,"width":1000,"height":1000,"xaxis":{"title":{"text":"Bin Midpoints (seconds)"},"gridcolor":"lightgray"},"yaxis":{"title":{"text":"Counts"},"gridcolor":"lightgray"},"barmode":"overlay"},"config":{}});
+            await Plotly.newPlot(graph_div, 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         </script>
     </div>
 </body>
diff --git a/examples/out_hist.svg b/examples/out_hist.svg
index cf5c69d..05f62b3 100644
--- a/examples/out_hist.svg
+++ b/examples/out_hist.svg
@@ -1 +1 @@
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opacity: 1; stroke-width: 0px; fill: rgb(0, 0, 0); fill-opacity: 1;"/></g><g class="point"><path d="M3.66,820V652.25H3.66V820Z" style="vector-effect: non-scaling-stroke; opacity: 1; stroke-width: 0px; fill: rgb(0, 0, 0); fill-opacity: 1;"/></g><g class="point"><path d="M3.66,820V643.9H3.66V820Z" style="vector-effect: non-scaling-stroke; opacity: 1; stroke-width: 0px; fill: rgb(0, 0, 0); fill-opacity: 1;"/></g></g></g></g></g><g class="overplot"/><path class="xlines-above crisp" d="M0,0" style="fill: none;"/><path class="ylines-above crisp" d="M0,0" style="fill: none;"/><g class="overlines-above"/><g class="xaxislayer-above"><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(83.65,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">0</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(164.67000000000002,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">10M</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(245.69,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">20M</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(326.71000000000004,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">30M</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(407.73,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">40M</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(488.75,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); 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fill-opacity: 1; white-space: pre;">0</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,778.96)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">5k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,637.92)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">10k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,496.88)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">15k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,355.83000000000004)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">20k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,214.79000000000002)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">25k</text></g></g><g class="overaxes-above"/></g></g><g class="polarlayer"/><g class="ternarylayer"/><g class="geolayer"/><g class="funnelarealayer"/><g class="pielayer"/><g class="treemaplayer"/><g class="sunburstlayer"/><g class="glimages"/><defs id="topdefs-fe10c7"><g class="clips"/><clipPath id="legendfe10c7"><rect width="162" height="48" x="0" y="0"/></clipPath></defs><g class="layer-above"><g class="imagelayer"/><g class="shapelayer"/></g><g class="infolayer"><g class="legend" pointer-events="all" transform="translate(825.62,100)"><rect class="bg" shape-rendering="crispEdges" style="stroke: rgb(68, 68, 68); stroke-opacity: 1; fill: rgb(255, 255, 255); fill-opacity: 1; stroke-width: 0px;" width="162" height="48" x="0" y="0"/><g class="scrollbox" transform="" clip-path="url('#legendfe10c7')"><g class="groups"><g class="traces" transform="translate(0,14.5)" style="opacity: 1;"><text class="legendtext" text-anchor="start" x="40" y="4.680000000000001" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">Frequency (nu_eff)</text><g class="layers" style="opacity: 1;"><g class="legendfill"/><g class="legendlines"/><g class="legendsymbols"><g class="legendpoints"><path class="legendundefined" d="M6,6H-6V-6H6Z" transform="translate(20,0)" style="stroke-width: 0px; fill: rgb(70, 130, 180); fill-opacity: 1;"/></g></g></g><rect class="legendtoggle" x="0" y="-9.5" width="157" height="19" style="fill: rgb(0, 0, 0); fill-opacity: 0;"/></g><g class="traces" transform="translate(0,33.5)" style="opacity: 1;"><text class="legendtext" text-anchor="start" x="40" y="4.680000000000001" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">Frequency (nu_meta)</text><g class="layers" style="opacity: 1;"><g class="legendfill"/><g class="legendlines"/><g class="legendsymbols"><g class="legendpoints"><path class="legendundefined" d="M6,6H-6V-6H6Z" transform="translate(20,0)" style="stroke-width: 0px; 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fill-opacity: 1; white-space: pre;">0.1</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(595.52,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">0.12</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(684.52,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">0.14</text></g><g class="xtick"><text text-anchor="middle" x="0" y="933" transform="translate(773.51,0)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">0.16</text></g></g><g class="yaxislayer-above"><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,920)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">0</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,819.22)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">10k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,718.45)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">20k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,617.67)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">30k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,516.9)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">40k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,416.12)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">50k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,315.34000000000003)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">60k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,214.57)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">70k</text></g><g class="ytick"><text text-anchor="end" x="79" y="4.199999999999999" transform="translate(0,113.78999999999999)" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">80k</text></g></g><g class="overaxes-above"/></g></g><g class="polarlayer"/><g class="ternarylayer"/><g class="geolayer"/><g class="funnelarealayer"/><g class="pielayer"/><g class="treemaplayer"/><g class="sunburstlayer"/><g class="glimages"/><defs id="topdefs-87c680"><g class="clips"/><clipPath id="legend87c680"><rect width="162" height="48" x="0" y="0"/></clipPath></defs><g class="layer-above"><g class="imagelayer"/><g class="shapelayer"/></g><g class="infolayer"><g class="legend" pointer-events="all" transform="translate(825.62,100)"><rect class="bg" shape-rendering="crispEdges" style="stroke: rgb(68, 68, 68); stroke-opacity: 1; fill: rgb(255, 255, 255); fill-opacity: 1; stroke-width: 0px;" width="162" height="48" x="0" y="0"/><g class="scrollbox" transform="" clip-path="url('#legend87c680')"><g class="groups"><g class="traces" transform="translate(0,14.5)" style="opacity: 1;"><text class="legendtext" text-anchor="start" x="40" y="4.680000000000001" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">Frequency (nu_eff)</text><g class="layers" style="opacity: 1;"><g class="legendfill"/><g class="legendlines"/><g class="legendsymbols"><g class="legendpoints"><path class="legendundefined" d="M6,6H-6V-6H6Z" transform="translate(20,0)" style="stroke-width: 0px; fill: rgb(70, 130, 180); fill-opacity: 1;"/></g></g></g><rect class="legendtoggle" x="0" y="-9.5" width="157" height="19" style="fill: rgb(0, 0, 0); fill-opacity: 0;"/></g><g class="traces" transform="translate(0,33.5)" style="opacity: 1;"><text class="legendtext" text-anchor="start" x="40" y="4.680000000000001" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 12px; fill: rgb(68, 68, 68); fill-opacity: 1; white-space: pre;">Frequency (nu_meta)</text><g class="layers" style="opacity: 1;"><g class="legendfill"/><g class="legendlines"/><g class="legendsymbols"><g class="legendpoints"><path class="legendundefined" d="M6,6H-6V-6H6Z" transform="translate(20,0)" style="stroke-width: 0px; fill: rgb(0, 0, 0); fill-opacity: 1;"/></g></g></g><rect class="legendtoggle" x="0" y="-9.5" width="157" height="19" style="fill: rgb(0, 0, 0); fill-opacity: 0;"/></g></g></g><rect class="scrollbar" rx="20" ry="3" width="0" height="0" style="fill: rgb(128, 139, 164); fill-opacity: 1;" x="0" y="0"/></g><g class="g-gtitle"><text class="gtitle" x="500" y="50" text-anchor="middle" dy="0em" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 17px; fill: rgb(68, 68, 68); opacity: 1; font-weight: normal; white-space: pre;">Final \nu_{eff}</text></g><g class="g-xtitle"><text class="xtitle" x="445.5" y="972" text-anchor="middle" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 14px; fill: rgb(68, 68, 68); opacity: 1; font-weight: normal; white-space: pre;">Bin Midpoints (seconds)</text></g><g class="g-ytitle"><text class="ytitle" transform="rotate(-90,42,510)" x="42" y="510" text-anchor="middle" style="font-family: 'Open Sans', verdana, arial, sans-serif; font-size: 14px; fill: rgb(68, 68, 68); opacity: 1; font-weight: normal; white-space: pre;">Counts</text></g></g></svg>
\ No newline at end of file
diff --git a/pyproject.toml b/pyproject.toml
index de872f9..b6ce66f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,7 +13,7 @@ classifiers = [
 dynamic = ["version"]
 dependencies = [
     "numpy>=2.2.0",
-    "matplotlib"
+    "matplotlib>=3.10"
 ]
 
 [project.optional-dependencies]
diff --git a/python_wrap/src/lib.rs b/python_wrap/src/lib.rs
index b9e6501..2dd7fa8 100644
--- a/python_wrap/src/lib.rs
+++ b/python_wrap/src/lib.rs
@@ -122,11 +122,18 @@ impl PythonPostProcess {
     #[new]
     #[pyo3(signature = (folder, root=None))]
     fn new(folder: &str, root: Option<String>) -> PyResult<Self> {
-        if let Ok(pp) = PostProcess::new(folder, root) {
-            return Ok(Self { inner: pp });
-        }
+        // if let Ok(pp) = PostProcess::new(folder, root) {
+        //     return Ok(Self { inner: pp });
+        // }
 
-        Err(PyValueError::new_err("Error creating object"))
+    
+        match PostProcess::new(folder, root) 
+        {
+            Ok(pp) => {Ok(Self { inner: pp })},
+            Err(err)=>{
+                println!("{:?}",err);
+                Err(PyValueError::new_err("Error creating object"))}
+        }
     }
 
     fn get_property_names(&self) -> PyResult<Vec<String>> {
@@ -230,9 +237,12 @@ impl PythonPostProcess {
         panic!("")
     }
 
-    fn get_spatial_property(&self, name: &str) -> PyResult<PyObject> {
+    fn get_spatial_property(&self, py: Python<'_>,name: &str) -> Py<PyArray2<f64>>{
         // TODO
-        Python::with_gil(|py| Ok(PyList::empty(py).to_object(py)))
+        match self.inner.get_spatial_average_property(name) {
+            Ok(e) => PyArray2::from_owned_array(py, e).unbind(),
+            Err(e) => panic!("{}", e),
+        }
     }
 
     fn get_biomass_concentration(&self, py: Python<'_>) -> Py<PyArray2<f64>> {
@@ -254,9 +264,13 @@ impl PythonPostProcess {
         PyArray2::from_owned_array(py, e).unbind()
     }
 
-    fn get_rtd(&self, flow: f64, step: f64, is_str: Option<bool>) -> PyResult<PyObject> {
-        // todo
-        Python::with_gil(|py| Ok(py.None()))
+    fn get_probes(&self, py: Python<'_>) -> Py<PyArray1<f64>> {
+        match self.inner.get_probes() {
+            Ok(e) => PyArray1::from_owned_array(py, e).unbind(),
+            Err(e) => panic!("{}", e),
+        }
+
+       
     }
 
     fn get_properties(&self, py: Python<'_>, key: &str, i_export: usize) -> Py<PyArray1<f64>> {

From 7903ffa1a5bb97a2ba5af102eec11da2b01d5bf2 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Fri, 2 May 2025 13:48:43 +0200
Subject: [PATCH 04/14] doc: improve docstring

---
 core/src/api.rs           | 14 +++++++++++++-
 core/src/datamodel/mod.rs | 18 ------------------
 core/src/impl_unique.rs   |  3 ++-
 3 files changed, 15 insertions(+), 20 deletions(-)

diff --git a/core/src/api.rs b/core/src/api.rs
index 6cbe99e..f441bdd 100644
--- a/core/src/api.rs
+++ b/core/src/api.rs
@@ -27,8 +27,16 @@ pub trait PostProcessReader {
     /// * `&[f64]` - A slice containing the time data.
     fn time(&self) -> &[f64];
 
+    /// Returns a weight chosen for simulation 
+    ///
+    /// # Returns
+    /// * `Weight object: Can contain either float (unique weight) or vector of weight (non implemented yet)
     fn weight(&self) -> &Weight;
 
+    // Returns tallies if exported during simulation 
+    ///
+    /// # Returns
+    /// * `Option<&Tallies>: Some if tallies exported 
     fn tallies(&self) -> Option<&Tallies>;
 
     /// Returns a 1D array view of the time data from the simulation results.
@@ -53,7 +61,11 @@ pub trait PostProcessReader {
     /// # Returns
     /// * `usize` - The total number of export events.
     fn n_export(&self) -> usize;
-
+    
+    /// Returns model's property names  
+    ///
+    /// # Returns
+    /// * `Vec<String>: Names, empty if no exported names  
     fn get_property_names(&self) -> Vec<String>;
 
     /// Computes the spatial average concentration for a specific species and phase.
diff --git a/core/src/datamodel/mod.rs b/core/src/datamodel/mod.rs
index 8e892e4..925fe90 100644
--- a/core/src/datamodel/mod.rs
+++ b/core/src/datamodel/mod.rs
@@ -97,24 +97,6 @@ pub fn f_get_probes(files: &[String]) -> Result<Array1<f64>, ApiError> {
 
     for filename in files.iter() {
         let file = hdf5::File::open(filename)?;
-        // if let Ok(dataset) = file.dataset("probes") {
-        //     let temp_array: Vec<f64> = match dataset.read_raw::<f64>() {
-        //         Ok(data) => data,
-        //         Err(_) => return None,
-        //     };
-
-        //     let tmp_array = match ArrayView1::from_shape(temp_array.len(), &temp_array) {
-        //         Ok(view) => view,
-        //         Err(_) => return None,
-        //     };
-
-        //     probe
-        //         .slice_mut(s![offset..offset + temp_array.len()])
-        //         .assign(&tmp_array);
-        //     offset += temp_array.len();
-        // } else {
-        //     return None;
-        // }
         let dataset = file.dataset("probes")?;
         let temp_array: Vec<f64> = dataset.read_raw::<f64>()?;
         let tmp_array = match ArrayView1::from_shape(temp_array.len(), &temp_array) {
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index 9edeca3..e7873e7 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -169,7 +169,7 @@ impl PostProcessReader for PostProcess {
     fn get_time_average_concentration(
         &self,
         species: usize,
-        position: usize,
+        position: usize, 
         phase: Phase,
     ) -> Result<Array1<f64>, ApiError> {
         let r = &self.results.main.records;
@@ -193,6 +193,7 @@ impl PostProcessReader for PostProcess {
         }
     }
 
+    //Actually compute spatial average property cannot be use to follow distribution  
     fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>
     {
         let nt: usize = self.results.main.records.time.len(); // Number of time steps

From 60bbd09a033d685d930e27a1bf8ff9b735de6aa3 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Fri, 2 May 2025 13:52:37 +0200
Subject: [PATCH 05/14] Use ApiError to error propagation (to improve)

---
 core/src/datamodel/_impl.rs |  4 ++--
 core/src/impl_unique.rs     | 10 +++-------
 2 files changed, 5 insertions(+), 9 deletions(-)

diff --git a/core/src/datamodel/_impl.rs b/core/src/datamodel/_impl.rs
index 25f1217..a00aa00 100644
--- a/core/src/datamodel/_impl.rs
+++ b/core/src/datamodel/_impl.rs
@@ -67,7 +67,7 @@ pub fn read_spatial_model_properties(
     files: &[String],
     cx: &mut Array2<f64>,
     n_export: usize,
-) -> hdf5::Result<()> {
+) -> Result<(), ApiError> {
     for filename in files.iter() {
         // Open the HDF5 file in read mode
         let file = hdf5::File::open_as(filename, hdf5::file::OpenMode::Read)?;
@@ -230,7 +230,7 @@ pub fn read_model_mass(
     files: &[String],
     cx: &mut Array2<f64>,
     n_export: usize,
-) -> hdf5::Result<()> {
+) -> Result<(), ApiError> {
     read_spatial_model_properties("mass", files, cx, n_export)
 }
 
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index e7873e7..341c325 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -206,10 +206,8 @@ impl PostProcessReader for PostProcess {
             return Err(ApiError::KeyError(key.to_string()));
         }
 
-        // Attempt to read model mass
-        if let Err(err) = read_spatial_model_properties(key,self.results.get_files(), &mut biomass_matrix, nt) {
-            return Err(ApiError::Io(err));
-        }
+        read_spatial_model_properties(key,self.results.get_files(), &mut biomass_matrix, nt) ?;
+     
 
 
         // Calculate biomass concentration
@@ -239,9 +237,7 @@ impl PostProcessReader for PostProcess {
         }
 
         // Attempt to read model mass
-        if let Err(err) = read_model_mass(self.results.get_files(), &mut biomass_matrix, nt) {
-            return Err(ApiError::Io(err));
-        }
+        read_model_mass(self.results.get_files(), &mut biomass_matrix, nt)?;
 
         // Convert volume to an array view
         let volume =

From 819f899c7de6c4963d708127e6e45cad1fa4d133 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 7 May 2025 13:43:05 +0200
Subject: [PATCH 06/14] ci: test pyo3 version

---
 .github/workflows/CI.yml |   2 +-
 Cargo.lock               |  29 +--
 pyproject.toml           |   2 +-
 python_wrap/Cargo.toml   |   4 +-
 uv.lock                  | 434 ++++++++++++++++++++++++++++++++++++++-
 5 files changed, 450 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 79edc5f..fcf44c4 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -40,7 +40,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: 3.x
+          python-version: 3.12
       - name: Install system dependencies
         run: |
           sudo apt-get update
diff --git a/Cargo.lock b/Cargo.lock
index 5a57654..998dc60 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -843,9 +843,9 @@ dependencies = [
 
 [[package]]
 name = "numpy"
-version = "0.23.0"
+version = "0.24.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b94caae805f998a07d33af06e6a3891e38556051b8045c615470a71590e13e78"
+checksum = "a7cfbf3f0feededcaa4d289fe3079b03659e85c5b5a177f4ba6fb01ab4fb3e39"
 dependencies = [
  "libc",
  "ndarray 0.16.1",
@@ -853,6 +853,7 @@ dependencies = [
  "num-integer",
  "num-traits",
  "pyo3",
+ "pyo3-build-config",
  "rustc-hash",
 ]
 
@@ -1008,9 +1009,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.23.3"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e484fd2c8b4cb67ab05a318f1fd6fa8f199fcc30819f08f07d200809dba26c15"
+checksum = "e5203598f366b11a02b13aa20cab591229ff0a89fd121a308a5df751d5fc9219"
 dependencies = [
  "cfg-if",
  "indoc",
@@ -1026,9 +1027,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.23.3"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dc0e0469a84f208e20044b98965e1561028180219e35352a2afaf2b942beff3b"
+checksum = "99636d423fa2ca130fa5acde3059308006d46f98caac629418e53f7ebb1e9999"
 dependencies = [
  "once_cell",
  "target-lexicon",
@@ -1036,9 +1037,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.23.3"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "eb1547a7f9966f6f1a0f0227564a9945fe36b90da5a93b3933fc3dc03fae372d"
+checksum = "78f9cf92ba9c409279bc3305b5409d90db2d2c22392d443a87df3a1adad59e33"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -1046,9 +1047,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.23.3"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "fdb6da8ec6fa5cedd1626c886fc8749bdcbb09424a86461eb8cdf096b7c33257"
+checksum = "0b999cb1a6ce21f9a6b147dcf1be9ffedf02e0043aec74dc390f3007047cecd9"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -1058,9 +1059,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.23.3"
+version = "0.24.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "38a385202ff5a92791168b1136afae5059d3ac118457bb7bc304c197c2d33e7d"
+checksum = "822ece1c7e1012745607d5cf0bcb2874769f0f7cb34c4cde03b9358eb9ef911a"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -1377,9 +1378,9 @@ dependencies = [
 
 [[package]]
 name = "target-lexicon"
-version = "0.12.16"
+version = "0.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
+checksum = "e502f78cdbb8ba4718f566c418c52bc729126ffd16baee5baa718cf25dd5a69a"
 
 [[package]]
 name = "thiserror"
diff --git a/pyproject.toml b/pyproject.toml
index b6ce66f..add9152 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,7 +18,7 @@ dependencies = [
 
 [project.optional-dependencies]
 vtk = [
-  'cmtool>=1.0.0',
+#  'cmtool>=1.0.0',
     'vtk==9.3.0',
 ]
 
diff --git a/python_wrap/Cargo.toml b/python_wrap/Cargo.toml
index 611f8f3..f8692bd 100644
--- a/python_wrap/Cargo.toml
+++ b/python_wrap/Cargo.toml
@@ -16,8 +16,8 @@ bindings = "pyo3"
 
 [dependencies]
 bcore = { path = "../core" }
-numpy = "0.23.0"
-pyo3 = { version = "0.23.1", features = ["extension-module"] }
+numpy = "0.24.0"
+pyo3 = { version = "0.24.2", features = ["extension-module"] }
 
 
 [lib]
diff --git a/uv.lock b/uv.lock
index ed0fc07..42fd743 100644
--- a/uv.lock
+++ b/uv.lock
@@ -1,16 +1,282 @@
 version = 1
-requires-python = ">=3.12"
+requires-python = ">=3.10"
 
 [[package]]
 name = "biomc-pp"
-version = "0.1.0"
+version = "0.4.2"
 source = { editable = "." }
 dependencies = [
+    { name = "matplotlib" },
     { name = "numpy" },
 ]
 
+[package.optional-dependencies]
+vtk = [
+    { name = "vtk" },
+]
+
 [package.metadata]
-requires-dist = [{ name = "numpy", specifier = ">=2.2.0" }]
+requires-dist = [
+    { name = "matplotlib", specifier = ">=3.10" },
+    { name = "numpy", specifier = ">=2.2.0" },
+    { name = "vtk", marker = "extra == 'vtk'", specifier = "==9.3.0" },
+]
+
+[[package]]
+name = "contourpy"
+version = "1.3.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "numpy" },
+]
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+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "matplotlib" },
+]
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/80/bb/2308cfd512ebb6b97173105fc27faa71b948136b331bd7d341349eb7e468/vtk-9.3.0-cp310-cp310-macosx_10_10_x86_64.whl", hash = "sha256:7d3492cb6c52b23dc0c6e664938b8119254a77b5e3099106e2567ed0b6473162", size = 76476756 },
+    { url = "https://files.pythonhosted.org/packages/13/36/3b4bb5d9073d682ccf31d5bb6d06c3275bcfc379ed2fc1d730c28a6ba303/vtk-9.3.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:e3f4e86bff7a4cd71bd6205bd18cf4b6ab70956ecf9cbd73e77a95b2210d98ef", size = 70111274 },
+    { url = "https://files.pythonhosted.org/packages/c4/66/23118087ce6bb1914ce367638b6113d827f2257b76ca506a06e288c0e13b/vtk-9.3.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:a827fb5f05ab78b2cbad81f5d3a3d7065fa995cc907cecdfa7a7b76374130ef3", size = 91995386 },
+    { url = "https://files.pythonhosted.org/packages/d8/ac/248a646b83fea3b910ac3cb08f0ce6ab2cb118de3e673bd266bc5f472a0c/vtk-9.3.0-cp310-cp310-win_amd64.whl", hash = "sha256:2aae778297817335ddd6698b4c124c109d8ac476512691fe19446614ae43ba56", size = 52422442 },
+    { url = "https://files.pythonhosted.org/packages/7a/86/bcd5dc64141d90604bc5a9efcb6f0a2a11983e6c001a2d9d9e0bbb4fedcf/vtk-9.3.0-cp311-cp311-macosx_10_10_x86_64.whl", hash = "sha256:a3cd59108b21f55b873a63878a0decec0a707bd960b59d5e15b37d1ad873590f", size = 76476999 },
+    { url = "https://files.pythonhosted.org/packages/c2/45/ffb4e2fc07c12f772cfddeb095f0a9a72bad7097c7ab0f08a292fc474be1/vtk-9.3.0-cp311-cp311-macosx_11_0_arm64.whl", hash = "sha256:6d2bdd2c60f0fa5d1926c11b72d96dc23caf9ff41781bae76e48edd09fb8aa03", size = 70111238 },
+    { url = "https://files.pythonhosted.org/packages/00/cf/e827806a34efe69ce286ba842605535c40b45ea338f8315dd0e0986e89a9/vtk-9.3.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3a02bf6067cae7abfd7f6b1330c69555b715be8ec71a3c8d6471af45a96e8e56", size = 91995090 },
+    { url = "https://files.pythonhosted.org/packages/0a/a5/c5e380300715cab30166d5ec9bba2ccabbf41452d3b09e2d7c1bfcfc11d5/vtk-9.3.0-cp311-cp311-win_amd64.whl", hash = "sha256:ff0eedcde5821c023623f70951f2499e9d59e709e288b67a2e2334abafacc322", size = 52420923 },
+    { url = "https://files.pythonhosted.org/packages/13/f1/f36b1978f1bee2323303207043a1c4b99387cfd2d9a8b7b6b79f0262d8a4/vtk-9.3.0-cp312-cp312-macosx_10_10_x86_64.whl", hash = "sha256:94678fa0476e113500f3b99e9692b92b83a5b058caace7bac3b5f780b12b36ed", size = 76620745 },
+    { url = "https://files.pythonhosted.org/packages/39/8d/d705ad84092cee806769084dca1cd143d296903854caaeb9164bbb0f595a/vtk-9.3.0-cp312-cp312-macosx_11_0_arm64.whl", hash = "sha256:371b96afca3ed41a0bf1cd80a42f4b906ca2f470a13df32f39b22a9169d996d7", size = 70146262 },
+    { url = "https://files.pythonhosted.org/packages/97/a6/91b79b1a4f90bcbd104613bc44a3038f6b63140554de211c71b8304d98a0/vtk-9.3.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5cfa8d73acbab386b9d6ef8a1a01149fd096a21a23547f10bf0cf98d88300724", size = 92039877 },
+    { url = "https://files.pythonhosted.org/packages/de/ca/0ba875f1924fc6b662c5c87a16d45604d3cc79fd1161bf8540b3096af941/vtk-9.3.0-cp312-cp312-win_amd64.whl", hash = "sha256:75d27b73270a42923ebefd87a8522f7717618c36825b8058c4d3aa8e64d6145d", size = 52426002 },
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From 8a9124aaee69e621f32a0b5c74acbad14c0368b5 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 7 May 2025 13:50:30 +0200
Subject: [PATCH 07/14] feat: add variance calculation

---
 core/src/api.rs         |  9 +++-
 core/src/impl_concat.rs | 12 +++++-
 core/src/impl_unique.rs | 73 ++++++++++++++++++++++++++------
 core/src/process/mod.rs | 12 +++++-
 python_wrap/src/lib.rs  | 93 ++++++++++++++++++++++++-----------------
 5 files changed, 143 insertions(+), 56 deletions(-)

diff --git a/core/src/api.rs b/core/src/api.rs
index f441bdd..5b439da 100644
--- a/core/src/api.rs
+++ b/core/src/api.rs
@@ -1,7 +1,7 @@
 use crate::datamodel::{Weight,tallies::Tallies};
 
 use crate::error::ApiError;
-use ndarray::{Array1, Array2, ArrayView3};
+use ndarray::{Array1, Array2, ArrayView2, ArrayView3};
 
 /// `Phase` enum represents different states or phases of a substance.
 #[derive(Clone, PartialEq, Copy)]
@@ -27,6 +27,8 @@ pub trait PostProcessReader {
     /// * `&[f64]` - A slice containing the time data.
     fn time(&self) -> &[f64];
 
+    fn v_liquid(&self) -> ArrayView2<'_, f64>;
+
     /// Returns a weight chosen for simulation 
     ///
     /// # Returns
@@ -86,6 +88,11 @@ pub trait PostProcessReader {
 
     fn get_spatial_average_mtr(&self, species: usize) -> Result<Array1<f64>, ApiError>;
 
+    fn get_variance_concentration(&self,species:usize,phase:Phase)-> Result<Array1<f64>, ApiError>;
+
+    
+    
+
     /// Computes the time average concentration for a specific species, position, and phase.
     ///
     /// # Arguments
diff --git a/core/src/impl_concat.rs b/core/src/impl_concat.rs
index a0e8fa7..1680ccd 100644
--- a/core/src/impl_concat.rs
+++ b/core/src/impl_concat.rs
@@ -2,7 +2,7 @@ use crate::api::PostProcessReader;
 use crate::datamodel::{Weight,tallies::Tallies};
 
 use crate::{api::Phase, error::ApiError, PostProcess};
-use ndarray::{Array1, Array2, ArrayView3, Axis};
+use ndarray::{Array1, Array2, ArrayView2, ArrayView3, Axis};
 
 #[derive(Debug)]
 pub struct ConcatPostPrcess {
@@ -47,6 +47,11 @@ impl PostProcessReader for ConcatPostPrcess {
         todo!()
     }
 
+    fn v_liquid(&self) -> ArrayView2<'_, f64>
+    {
+        todo!()
+    }
+
     fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>
     {
         todo!()
@@ -56,6 +61,11 @@ impl PostProcessReader for ConcatPostPrcess {
         todo!()
     }
 
+    fn get_variance_concentration(&self,species:usize,phase:Phase)-> Result<Array1<f64>, ApiError>
+    {
+        todo!()
+    }
+
     fn get_spatial_average_biomass_concentration(&self) -> Result<Array1<f64>, ApiError> {
         let mut concatenated = Array1::<f64>::default(0);
         for postprocess in &self.dataset {
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index 341c325..4071019 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -1,12 +1,14 @@
 use crate::api::{ModelEstimator, PostProcessReader};
+use crate::datamodel::{f_get_probes, make_histogram, read_spatial_model_properties, Results};
 use crate::datamodel::{
     get_n_export_real, read_avg_model_properties, read_model_mass, read_model_properties,
-    vec_to_array_view2, vec_to_array_view3, Dim, tallies::Tallies, Weight,
+    tallies::Tallies, vec_to_array_view2, vec_to_array_view3, Dim, Weight,
+};
+use crate::process::{
+    normalize_concentration, spatial_average_concentration, variance_concentration, Histogram,
 };
-use crate::datamodel::{f_get_probes, make_histogram, read_spatial_model_properties, Results};
-use crate::process::{spatial_average_concentration, Histogram};
 use crate::{api::Estimator, api::Phase, error::ApiError};
-use ndarray::{s, Array1, Array2, ArrayView3, Axis};
+use ndarray::{s, Array1, Array2, ArrayView1, ArrayView2, ArrayView3, Axis};
 
 /// The `PostProcess` struct handles post-processing of simulation results.
 ///
@@ -67,6 +69,55 @@ impl PostProcessReader for PostProcess {
         // let mtr = vec_to_array_view3(self.results., &dim, nt);
     }
 
+    fn v_liquid(&self) -> ArrayView2<'_, f64> {
+        let nt = self.results.main.records.time.len();
+        let dim = &self.results.main.records.dim;
+        vec_to_array_view2(&self.results.main.records.volume_liquid, nt, dim.0)
+    }
+
+    fn get_variance_concentration(
+        &self,
+        species: usize,
+        phase: Phase,
+    ) -> Result<Array1<f64>, ApiError> {
+        // Helper
+        fn process_phase(
+            concentration: &Vec<f64>,
+            volume: &Vec<f64>,
+            nt: usize,
+            dim: &Dim,
+            species: usize,
+        ) -> Array1<f64> {
+            let c: ndarray::ArrayBase<ndarray::ViewRepr<&f64>, ndarray::Dim<[usize; 3]>> =
+                vec_to_array_view3(concentration, dim, nt);
+            let vol = vec_to_array_view2(volume, nt, dim.0);
+            let c_slice = &c.slice(s![.., .., species]);
+            let normalized_c = variance_concentration(&c_slice, &vol);
+            normalized_c
+        }
+
+        let records = &self.results.main.records;
+        let nt = records.time.len();
+        let dim = &records.dim;
+
+        match phase {
+            Phase::Gas => {
+                if let (Some(c), Some(v)) = (&records.concentration_gas, &records.volume_gas) {
+                    return Ok(process_phase(c, v, nt, dim, species));
+                }
+
+                panic!("Gas is not present");
+            }
+            Phase::Liquid => Ok(process_phase(
+                &records.concentration_liquid,
+                &records.volume_liquid,
+                nt,
+                dim,
+                species,
+            )),
+        }
+    }
+
     /// Returns an `ArrayView1<f64>` representing the time data from the simulation results.
     ///
     /// # Returns
@@ -169,7 +220,7 @@ impl PostProcessReader for PostProcess {
     fn get_time_average_concentration(
         &self,
         species: usize,
-        position: usize, 
+        position: usize,
         phase: Phase,
     ) -> Result<Array1<f64>, ApiError> {
         let r = &self.results.main.records;
@@ -193,9 +244,8 @@ impl PostProcessReader for PostProcess {
         }
     }
 
-    //Actually compute spatial average property cannot be use to follow distribution  
-    fn get_spatial_average_property(&self, key:&str) ->  Result<Array2<f64>, ApiError>
-    {
+    //Actually compute spatial average property cannot be use to follow distribution
+    fn get_spatial_average_property(&self, key: &str) -> Result<Array2<f64>, ApiError> {
         let nt: usize = self.results.main.records.time.len(); // Number of time steps
         let num_dimensions = self.results.main.records.dim.0; // Dimensionality
 
@@ -206,9 +256,7 @@ impl PostProcessReader for PostProcess {
             return Err(ApiError::KeyError(key.to_string()));
         }
 
-        read_spatial_model_properties(key,self.results.get_files(), &mut biomass_matrix, nt) ?;
-     
-
+        read_spatial_model_properties(key, self.results.get_files(), &mut biomass_matrix, nt)?;
 
         // Calculate biomass concentration
         biomass_matrix /= self.get_number_particle();
@@ -216,8 +264,7 @@ impl PostProcessReader for PostProcess {
         Ok(biomass_matrix)
     }
 
-    fn get_probes(&self) -> Result<Array1<f64>, ApiError>
-    {
+    fn get_probes(&self) -> Result<Array1<f64>, ApiError> {
         f_get_probes(&self.results.files)
     }
 
diff --git a/core/src/process/mod.rs b/core/src/process/mod.rs
index c65bbfe..b63b231 100644
--- a/core/src/process/mod.rs
+++ b/core/src/process/mod.rs
@@ -21,11 +21,19 @@ pub fn normalize_concentration(
 }
 
 pub fn variance_concentration(
-    mean_concentration: &ArrayView1<f64>,
     concentration_record: &ArrayView2<f64>,
     full_volume: &ArrayView2<f64>,
 ) -> Array1<f64> {
-    let mean_concentration = spatial_average_concentration(concentration_record, full_volume);
+    let mean_concentration = spatial_average_concentration(concentration_record, full_volume).insert_axis(Axis(1));    
+    ((concentration_record - mean_concentration).powi(2) * full_volume).sum_axis(Axis(1))
+}
+
+
+pub fn variance_concentration_from_mean(
+    concentration_record: &ArrayView2<f64>,
+    mean_concentration: &ArrayView1<f64>,
+    full_volume: &ArrayView2<f64>,
+) -> Array1<f64> {
     ((concentration_record - mean_concentration).pow2() * full_volume).sum_axis(Axis(1))
 }
 
diff --git a/python_wrap/src/lib.rs b/python_wrap/src/lib.rs
index 2dd7fa8..1360c84 100644
--- a/python_wrap/src/lib.rs
+++ b/python_wrap/src/lib.rs
@@ -1,11 +1,11 @@
 use bcore::api::ModelEstimator;
+use bcore::Weight;
 use bcore::{PostProcess, PostProcessReader};
 use numpy::PyArray2;
 use numpy::{PyArray1, PyArray3};
 use pyo3::exceptions::{PyRuntimeError, PyValueError};
 use pyo3::prelude::*;
 use pyo3::types::PyList;
-use bcore::Weight;
 /// A struct that wraps the `PostProcess` type for Python bindings.
 ///
 /// The `PythonPostProcess` struct is designed to provide a Python interface for the
@@ -59,7 +59,6 @@ impl From<bcore::api::Phase> for Phase {
     }
 }
 
-
 /// An enum representing different phases .
 /// # Example
 /// ```python
@@ -91,7 +90,6 @@ impl From<bcore::api::Estimator> for Estimator {
     }
 }
 
-
 #[pymethods]
 impl PythonPostProcess {
     /// Creates a new instance of `PythonPostProcess`.
@@ -126,13 +124,12 @@ impl PythonPostProcess {
         //     return Ok(Self { inner: pp });
         // }
 
-    
-        match PostProcess::new(folder, root) 
-        {
-            Ok(pp) => {Ok(Self { inner: pp })},
-            Err(err)=>{
-                println!("{:?}",err);
-                Err(PyValueError::new_err("Error creating object"))}
+        match PostProcess::new(folder, root) {
+            Ok(pp) => Ok(Self { inner: pp }),
+            Err(err) => {
+                println!("{:?}", err);
+                Err(PyValueError::new_err("Error creating object"))
+            }
         }
     }
 
@@ -140,6 +137,13 @@ impl PythonPostProcess {
         Ok(self.inner.get_property_names())
     }
 
+    #[getter]
+    fn v_liquid(&self, py: Python<'_>)-> Py<PyArray2<f64>>
+    {
+        let e = self.inner.v_liquid().to_owned();
+        PyArray2::from_owned_array(py, e).unbind()
+    }
+
     /// Gets the time data
     ///
     /// This function provides access to the time data stored within the `PostProcess` object.
@@ -185,14 +189,11 @@ impl PythonPostProcess {
     }
 
     #[getter]
-    fn weight(&self,py: Python<'_>) -> Py<PyArray1<f64>> {
-        match self.inner.weight()
-        {
-            Weight::Single(sw)=>{PyArray1::from_vec(py, vec![*sw]).unbind()},
-            Weight::Multiple(mw)=>{PyArray1::from_vec(py, mw.clone()).unbind()}
+    fn weight(&self, py: Python<'_>) -> Py<PyArray1<f64>> {
+        match self.inner.weight() {
+            Weight::Single(sw) => PyArray1::from_vec(py, vec![*sw]).unbind(),
+            Weight::Multiple(mw) => PyArray1::from_vec(py, mw.clone()).unbind(),
         }
-
-        
     }
 
     fn get_spatial_average_concentration(
@@ -208,6 +209,19 @@ impl PythonPostProcess {
         PyArray1::from_owned_array(py, e).unbind()
     }
 
+    fn get_variance_concentration(
+        &self,
+        py: Python<'_>,
+        species: usize,
+        phase: Phase,
+    ) -> Py<PyArray1<f64>> {
+        if let Ok(e) = self.inner.get_variance_concentration(species, phase.into()) {
+            PyArray1::from_owned_array(py, e).unbind()
+        } else {
+            panic!("get_variance_concentration")
+        }
+    }
+
     fn get_spatial_average_mtr(&self, py: Python<'_>, species: usize) -> Py<PyArray1<f64>> {
         match self.inner.get_spatial_average_mtr(species) {
             Ok(e) => PyArray1::from_owned_array(py, e).unbind(),
@@ -228,16 +242,16 @@ impl PythonPostProcess {
         position: usize,
         phase: Phase,
     ) -> Py<PyArray1<f64>> {
-        if let Ok(e) =
-            self.inner
-                .get_time_average_concentration(species, position, phase.into())
+        if let Ok(e) = self
+            .inner
+            .get_time_average_concentration(species, position, phase.into())
         {
             return PyArray1::from_owned_array(py, e).unbind();
         }
         panic!("")
     }
 
-    fn get_spatial_property(&self, py: Python<'_>,name: &str) -> Py<PyArray2<f64>>{
+    fn get_spatial_property(&self, py: Python<'_>, name: &str) -> Py<PyArray2<f64>> {
         // TODO
         match self.inner.get_spatial_average_property(name) {
             Ok(e) => PyArray2::from_owned_array(py, e).unbind(),
@@ -269,8 +283,6 @@ impl PythonPostProcess {
             Ok(e) => PyArray1::from_owned_array(py, e).unbind(),
             Err(e) => panic!("{}", e),
         }
-
-       
     }
 
     fn get_properties(&self, py: Python<'_>, key: &str, i_export: usize) -> Py<PyArray1<f64>> {
@@ -320,42 +332,45 @@ impl PythonPostProcess {
         }
     }
 
-    pub fn estimate(&self, etype: Estimator, key: &str, i_export: usize) -> PyResult<f64> 
-    {
-        match self.inner.estimate(etype.into(),key,i_export) {
+    pub fn estimate(&self, etype: Estimator, key: &str, i_export: usize) -> PyResult<f64> {
+        match self.inner.estimate(etype.into(), key, i_export) {
             Ok(e) => Ok(e),
             Err(e) => Err(PyErr::new::<PyRuntimeError, _>(e.to_string())),
         }
     }
-    
-    fn get_spatial_average_biomass_concentration(&self,py: Python<'_>) -> PyResult<Py<PyArray1<f64>>>
-    {
+
+    fn get_spatial_average_biomass_concentration(
+        &self,
+        py: Python<'_>,
+    ) -> PyResult<Py<PyArray1<f64>>> {
         match self.inner.get_spatial_average_biomass_concentration() {
             Ok(e) => Ok(PyArray1::from_owned_array(py, e).unbind()),
             Err(e) => Err(PyErr::new::<PyRuntimeError, _>(e.to_string())),
         }
     }
 
-    pub fn estimate_time(&self, py: Python<'_>,etype: Estimator, key: &str) -> PyResult<Py<PyArray1<f64>>>
-    {
-        match self.inner.estimate_time(etype.into(),key) {
+    pub fn estimate_time(
+        &self,
+        py: Python<'_>,
+        etype: Estimator,
+        key: &str,
+    ) -> PyResult<Py<PyArray1<f64>>> {
+        match self.inner.estimate_time(etype.into(), key) {
             Ok(e) => Ok(PyArray1::from_owned_array(py, e).unbind()),
             Err(e) => Err(PyErr::new::<PyRuntimeError, _>(e.to_string())),
         }
     }
 
-    pub fn get_csv_tallies(&self, py: Python<'_>)->PyResult<String>
-    {
+    pub fn get_csv_tallies(&self, py: Python<'_>) -> PyResult<String> {
         match self.inner.tallies() {
             Some(e) => Ok(e.to_csv().unwrap()),
-            None=> Err(PyErr::new::<PyRuntimeError, _>("No data")),
+            None => Err(PyErr::new::<PyRuntimeError, _>("No data")),
         }
     }
 
     fn get_tallies(&self, py: Python<'_>) -> Py<PyArray2<f64>> {
         match self.inner.tallies() {
-            Some(e) => 
-            {
+            Some(e) => {
                 let v = e.to_array().to_owned();
                 PyArray2::from_owned_array(py, v).unbind()
             }
@@ -366,10 +381,10 @@ impl PythonPostProcess {
 
 #[pymodule]
 mod biomc_pp {
-    #[pymodule_export]
-    use super::Phase;
     #[pymodule_export]
     use super::Estimator;
     #[pymodule_export]
+    use super::Phase;
+    #[pymodule_export]
     use super::PythonPostProcess;
 }

From 1649f993a1a7e545b227f2b386d4b3c053fc7087 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 16:44:19 +0200
Subject: [PATCH 08/14] ci: add doc

---
 .github/workflows/pages.yml | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 .github/workflows/pages.yml

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
new file mode 100644
index 0000000..97c633d
--- /dev/null
+++ b/.github/workflows/pages.yml
@@ -0,0 +1,30 @@
+name: Deploy Documentation
+
+on:
+  push:
+    branches: [ main ] 
+  pull_request:
+    branches: [ main ]
+
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Rust
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          profile: minimal
+          override: true
+
+      - name: Generate Documentation
+        run: cargo doc --no-deps --document-private-items
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v3
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./target/doc

From b19ee335276454638beceae0c33e708d2cfd71b6 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 16:48:46 +0200
Subject: [PATCH 09/14] ci: remove dep from doc

---
 .github/workflows/pages.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
index 97c633d..9a0887e 100644
--- a/.github/workflows/pages.yml
+++ b/.github/workflows/pages.yml
@@ -21,7 +21,7 @@ jobs:
           override: true
 
       - name: Generate Documentation
-        run: cargo doc --no-deps --document-private-items
+        run: cargo doc --workspace --no-deps --document-private-items
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3

From 65623238124371e858a627aebc4fe45b0cfc9317 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 16:50:26 +0200
Subject: [PATCH 10/14] ci: remove dep from doc

---
 .github/workflows/pages.yml | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
index 9a0887e..7dd203e 100644
--- a/.github/workflows/pages.yml
+++ b/.github/workflows/pages.yml
@@ -13,6 +13,11 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y cmake libhdf5-dev
+
       - name: Install Rust
         uses: actions-rs/toolchain@v1
         with:

From 2a266780def1049a9289fabdbd6d9c41e7cdb7e8 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 16:53:03 +0200
Subject: [PATCH 11/14] ci: fix

---
 .github/workflows/pages.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
index 7dd203e..c00e10d 100644
--- a/.github/workflows/pages.yml
+++ b/.github/workflows/pages.yml
@@ -28,8 +28,10 @@ jobs:
       - name: Generate Documentation
         run: cargo doc --workspace --no-deps --document-private-items
 
-      - name: Deploy to GitHub Pages
-        uses: peaceiris/actions-gh-pages@v3
+      - name: Deploy Docs
+        uses: peaceiris/actions-gh-pages@v4
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_branch: gh-pages
           publish_dir: ./target/doc
+          force_orphan: true

From c919544d14a9b24ad7544369af320e70afde9a37 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 16:57:37 +0200
Subject: [PATCH 12/14] ci: fix

---
 .github/workflows/pages.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
index c00e10d..581a14a 100644
--- a/.github/workflows/pages.yml
+++ b/.github/workflows/pages.yml
@@ -1,5 +1,6 @@
 name: Deploy Documentation
-
+permissions:
+  contents: write
 on:
   push:
     branches: [ main ] 

From 8ff16d3fa8ac1ec987404d874b53fe55febb6c9e Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 17:11:13 +0200
Subject: [PATCH 13/14] chore: clippy

---
 Cargo.lock                      | 6 +++---
 Cargo.toml                      | 2 +-
 README.md                       | 1 +
 core/src/datamodel/main_file.rs | 1 -
 core/src/datamodel/mod.rs       | 4 ++--
 core/src/impl_unique.rs         | 8 ++++----
 examples/example_histogram.rs   | 3 +--
 examples/example_rust.rs        | 2 +-
 python_wrap/src/lib.rs          | 1 -
 9 files changed, 13 insertions(+), 15 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 998dc60..b8d4d3f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -81,7 +81,7 @@ dependencies = [
 
 [[package]]
 name = "bcore"
-version = "0.4.2"
+version = "0.4.4"
 dependencies = [
  "csv",
  "hdf5",
@@ -402,7 +402,7 @@ dependencies = [
 
 [[package]]
 name = "examples"
-version = "0.4.2"
+version = "0.4.4"
 dependencies = [
  "bcore",
  "ndarray 0.16.1",
@@ -1072,7 +1072,7 @@ dependencies = [
 
 [[package]]
 name = "python_wrap"
-version = "0.4.2"
+version = "0.4.4"
 dependencies = [
  "bcore",
  "numpy",
diff --git a/Cargo.toml b/Cargo.toml
index 08b55f6..e2cde31 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -7,7 +7,7 @@ members = [
 resolver = "2"
 
 [workspace.package]
-version = "0.4.2"
+version = "0.4.4"
 edition = "2021"
 license = "MIT"
 repository = "https://github.com/Benncs/BioMC_PostProcess/"
diff --git a/README.md b/README.md
index a985b6b..85de5f8 100644
--- a/README.md
+++ b/README.md
@@ -35,3 +35,4 @@ It also includes **PyO3 bindings** to provide a high-level Python API for end us
 ### LICENSE 
 
 
+This code is under [MIT](./LICENSE) license
\ No newline at end of file
diff --git a/core/src/datamodel/main_file.rs b/core/src/datamodel/main_file.rs
index 8714582..9e05f24 100644
--- a/core/src/datamodel/main_file.rs
+++ b/core/src/datamodel/main_file.rs
@@ -5,7 +5,6 @@
 
 use super::{tallies::Tallies, Dim, ResultGroup, Weight};
 use std::collections::HashMap;
-use ndarray::{ArrayView2};
 ///File's mics section
 #[derive(Debug)]
 pub struct Misc {
diff --git a/core/src/datamodel/mod.rs b/core/src/datamodel/mod.rs
index 925fe90..3237db2 100644
--- a/core/src/datamodel/mod.rs
+++ b/core/src/datamodel/mod.rs
@@ -165,7 +165,7 @@ mod tests {
     #[test]
     fn test_vec_to_array_view3() {
         let vec = vec![1.0; 6]; // 2 * 3 dimensions
-        let dim = &Dim { 0: 2, 1: 3 };
+        let dim = &Dim(2, 3);
         let nt = 1;
         let vec_copy = vec.clone();
         let array_view = vec_to_array_view3(&vec, dim, nt);
@@ -179,7 +179,7 @@ mod tests {
     #[should_panic]
     fn test_vec_to_array_view3_size_mismatch() {
         let vec = vec![1.0, 2.0, 3.0];
-        let dim = &Dim { 0: 2, 1: 3 };
+        let dim = &Dim(2, 3);
         let nt = 1;
 
         let _ = vec_to_array_view3(&vec, dim, nt);
diff --git a/core/src/impl_unique.rs b/core/src/impl_unique.rs
index 4071019..411a51a 100644
--- a/core/src/impl_unique.rs
+++ b/core/src/impl_unique.rs
@@ -5,10 +5,10 @@ use crate::datamodel::{
     tallies::Tallies, vec_to_array_view2, vec_to_array_view3, Dim, Weight,
 };
 use crate::process::{
-    normalize_concentration, spatial_average_concentration, variance_concentration, Histogram,
+    spatial_average_concentration, variance_concentration, Histogram,
 };
 use crate::{api::Estimator, api::Phase, error::ApiError};
-use ndarray::{s, Array1, Array2, ArrayView1, ArrayView2, ArrayView3, Axis};
+use ndarray::{s, Array1, Array2, ArrayView2, ArrayView3, Axis};
 
 /// The `PostProcess` struct handles post-processing of simulation results.
 ///
@@ -92,8 +92,8 @@ impl PostProcessReader for PostProcess {
                 vec_to_array_view3(concentration, dim, nt);
             let vol = vec_to_array_view2(volume, nt, dim.0);
             let c_slice = &c.slice(s![.., .., species]);
-            let normalized_c = variance_concentration(&c_slice, &vol);
-            normalized_c
+            
+            variance_concentration(c_slice, &vol)
         }
 
         let records = &self.results.main.records;
diff --git a/examples/example_histogram.rs b/examples/example_histogram.rs
index a22d03c..618f212 100644
--- a/examples/example_histogram.rs
+++ b/examples/example_histogram.rs
@@ -1,6 +1,5 @@
 use bcore::{PostProcess,PostProcessReader};
-use plotly::layout::{Shape, ShapeLine, ShapeType};
-use plotly::{ImageFormat, Scatter};
+use plotly::ImageFormat;
 use plotly::{Bar, Layout, Plot};
 
 fn main() {
diff --git a/examples/example_rust.rs b/examples/example_rust.rs
index b4ac290..a99dbdd 100644
--- a/examples/example_rust.rs
+++ b/examples/example_rust.rs
@@ -8,7 +8,7 @@ fn main() {
         Some("/home-local/casale/Documents/thesis/simulations/meta/out_str_nu_redis_2".to_string()),
     ) {
         let x = obj.get_biomass_concentration().unwrap();
-        let time: Vec<f64> = obj.time().into_iter().map(|t| t / 3600.).collect();
+        let time: Vec<f64> = obj.time().iter().map(|t| t / 3600.).collect();
         let xvec = x.slice(s![.., 0]).to_vec();
 
         let mut plot = Plot::new();
diff --git a/python_wrap/src/lib.rs b/python_wrap/src/lib.rs
index 1360c84..c498e2b 100644
--- a/python_wrap/src/lib.rs
+++ b/python_wrap/src/lib.rs
@@ -5,7 +5,6 @@ use numpy::PyArray2;
 use numpy::{PyArray1, PyArray3};
 use pyo3::exceptions::{PyRuntimeError, PyValueError};
 use pyo3::prelude::*;
-use pyo3::types::PyList;
 /// A struct that wraps the `PostProcess` type for Python bindings.
 ///
 /// The `PythonPostProcess` struct is designed to provide a Python interface for the

From f7bb956515ee2e0e6506360f0d9beeb614ca1656 Mon Sep 17 00:00:00 2001
From: Casale Benjamin <casale@insa-09720>
Date: Wed, 21 May 2025 17:15:48 +0200
Subject: [PATCH 14/14] chore: readme

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 85de5f8..c4cffdf 100644
--- a/README.md
+++ b/README.md
@@ -3,7 +3,7 @@
 
 
 ## Project Overview
-The **BioMC Postprocessor API** is a Rust module designed to facilitate interaction with post-processing simulation results via the BiomC API.  
+The **BioMC Postprocessor API** is a Rust API designed to interact with and perform post-processing on simulation results obtained with the [BioMC code](https://github.com/Benncs/BioCMA-MCST).  
 It also includes **PyO3 bindings** to provide a high-level Python API for end users.