small-fish-gui 1.9.1__tar.gz → 1.9.3__tar.gz

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.1
+Version: 1.9.3
 Summary: Small Fish is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 Project-URL: Homepage, https://github.com/2Echoes/small_fish
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
@@ -13,6 +13,7 @@ Requires-Python: >=3.8
 Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7
 Requires-Dist: czifile==2019.7.2
+Requires-Dist: freesimplegui==5.1.1
 Requires-Dist: imageio==2.34.0
 Requires-Dist: napari-console==0.0.9
 Requires-Dist: napari-plugin-engine==0.2.0
@@ -23,7 +24,6 @@ Requires-Dist: numpy==1.24.4
 Requires-Dist: openpyxl==3.1.2
 Requires-Dist: pandas==1.5.3
 Requires-Dist: pyarrow==11.0.0
-Requires-Dist: pysimplegui==4.60.5
 Requires-Dist: scikit-image==0.19.1
 Requires-Dist: scikit-learn==1.3.2
 Requires-Dist: scipy==1.9.1

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.9.1"
+version = "1.9.3"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]
@@ -28,7 +28,7 @@ dependencies = [
 "napari-svg==0.1.10",
 "numpy==1.24.4",
 "pandas==1.5.3",
-"PySimpleGUI==4.60.5",
+"FreeSimpleGUI==5.1.1",
 "scipy==1.9.1",
 "scikit-image==0.19.1",
 "scikit-learn==1.3.2",

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/README.md

@@ -1,3 +1,7 @@
+***INSTALATTION ISSUE : Currently the package cannot be installed due to a package deletion on pypi. I will migrate the code to a free, open source gui package and update the dependecies list***
+  
+  --> Requirements have been updated, pip installation is still not working but it is possible to install through git cloning
+
 # Small Fish
 **Small Fish** is a python application for the analysis of smFish images. It provides a ready to use graphical interface to combine famous python packages for cell analysis without any need for coding.
 
@@ -5,7 +9,7 @@ Cell segmentation (**2D**) is peformed using *cellpose* (published work) : https
 
 Spot detection is performed via *big-fish* (published work) : https://github.com/fish-quant/big-fish
 
-**Time stacks are not supported.**
+***Small Fish is bulding a [wiki](https://github.com/2Echoes/small_fish_gui/wiki) ! Make sure to check it out.***
 
 ## What can you do with small fish ?
 
@@ -93,5 +97,11 @@ Note that for training it is recommended to first set up your GPU as training co
 ## Developpement
 
 Optional features to include in future versions : 
+
+**Major Dev**
 - time stack (which would include cell tracking)
 - 3D segmentation
+
+**Minor features**
+- allows npz files with multiple masks in load segmentation by asking user which one to select
+- fix parquet format or replace to another compressed format

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/__init__.py

@@ -38,4 +38,4 @@ ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 """
-__version__ = "1.9.1"
+__version__ = "1.9.3"

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/__main__.py

@@ -1,5 +1,5 @@
 import sys, subprocess
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 
 from small_fish_gui import __version__
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/batch/integrity.py

@@ -6,7 +6,7 @@ import os
 import czifile as czi
 import bigfish.stack as stack
 import numpy as np
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 
 from ..pipeline._preprocess import check_integrity, convert_parameters_types, ParameterInputError, _check_segmentation_parameters
 from ..pipeline.segmentation import _cast_segmentation_parameters

small_fish_gui-1.9.3/src/small_fish_gui/batch/pipeline.py

@@ -0,0 +1,254 @@
+"""
+Submodule keeping necessary calls from main pipeline for batch processing.
+"""
+
+import os
+import pandas as pd
+import FreeSimpleGUI as sg
+
+from ..hints import pipeline_parameters
+
+from .input import open_image
+from ..interface import write_results
+from ..pipeline import reorder_shape, reorder_image_stack, prepare_image_detection
+from ..pipeline import cell_segmentation, launch_detection, launch_features_computation
+from ..pipeline import launch_spots_extraction
+from ..pipeline import get_nucleus_signal
+from ..pipeline import _cast_segmentation_parameters, convert_parameters_types
+from ..pipeline import plot_segmentation, output_spot_tiffvisual
+from ..utils import get_datetime
+
+def window_print(window: sg.Window, *args) :
+    print(*args)
+    window.refresh()
+
+def batch_pipeline(
+        batch_window : sg.Window,
+        batch_progress_bar : sg.ProgressBar,
+        progress_count : sg.Text,
+        parameters : pipeline_parameters,
+        filenames_list : list,
+        do_segmentation : bool,
+        map_ : dict,
+        results_df : pd.DataFrame,
+        cell_results_df : pd.DataFrame,
+        is_3D,
+        last_acquisition_id=0,
+) :
+    
+    #Extracting parameters
+    input_path = parameters['Batch_folder']
+    output_path = parameters['output_folder']
+    batch_name = parameters['batch_name']
+    time = '_' + get_datetime()
+
+    #Preparing folder
+    window_print(batch_window,"Creating folders for output...")
+    main_dir = output_path + "/" + batch_name + time + "/"
+    os.makedirs(main_dir + "results/", exist_ok=True)
+    if parameters['save segmentation'] : os.makedirs(main_dir + "segmentation/", exist_ok=True)
+    if parameters['save detection'] : os.makedirs(main_dir + "detection/", exist_ok=True)
+    if parameters['extract spots'] : os.makedirs(main_dir + "results/spots_extraction", exist_ok=True)
+
+    #Setting spot detection dimension
+    parameters['dim'] = 3 if is_3D else 2
+
+    #Pipeline loop
+    window_print(batch_window,"Launching batch analysis...")
+    batch_progress_bar.update(max=len(filenames_list))
+    filenames_list.sort()
+    
+
+    error_log = open(main_dir + "error_log", mode='w')
+    error_count = 0
+
+    for acquisition_id, file in enumerate(filenames_list) :
+        try :
+
+            #GUI
+            window_print(batch_window,"\nNext file : {0}".format(file))
+            batch_progress_bar.update(current_count= acquisition_id, max= len(filenames_list))
+            progress_count.update(value=str(acquisition_id))
+            batch_window = batch_window.refresh()
+
+            #0. Open image
+            image = open_image(input_path + '/' + file)
+            parameters['image'] = image
+            parameters['filename'] = file
+            for key_to_clean in [0,2] : 
+                if key_to_clean in parameters : del parameters[key_to_clean]
+
+            #1. Re-order shape
+            shape = image.shape
+            parameters['shape'] = shape
+            parameters['reordered_shape'] = reorder_shape(shape, map_=map_)
+
+            #2. Segmentation (opt)
+            if do_segmentation :
+                window_print(batch_window,"Segmenting cells...")
+                im_seg = reorder_image_stack(map_, image)
+                parameters = _cast_segmentation_parameters(parameters)
+                cytoplasm_label, nucleus_label = cell_segmentation(
+                    im_seg,
+                    cyto_model_name= parameters['cyto_model_name'],
+                    cyto_diameter= parameters['cytoplasm diameter'],
+                    nucleus_model_name= parameters['nucleus_model_name'],
+                    nucleus_diameter= parameters['nucleus diameter'],
+                    channels=[parameters['cytoplasm channel'], parameters['nucleus channel']],
+                    do_only_nuc=parameters['Segment only nuclei']
+                    )
+
+                parameters['segmentation_done'] = True
+
+                if cytoplasm_label.max() == 0 : #No cell segmented
+                    window_print(batch_window,"No cell was segmented, computing next image.")
+                    continue
+                else : 
+                    window_print(batch_window, "{0} cells segmented.".format(cytoplasm_label.max()))
+
+                    if parameters['save segmentation'] :
+                        plot_segmentation(
+                            cyto_image=im_seg[parameters['cytoplasm channel']],
+                            cyto_label= cytoplasm_label,
+                            nuc_image= im_seg[parameters['nucleus channel']],
+                            nuc_label=nucleus_label,
+                            path= main_dir + "segmentation/" + file,
+                            do_only_nuc= parameters['Segment only nuclei'],
+                        )
+
+            else :
+                cytoplasm_label, nucleus_label = None,None
+                parameters['segmentation_done'] = False
+
+            #3. Detection, deconvolution, clusterisation
+            window_print(batch_window,"Detecting spots...")
+            parameters = convert_parameters_types(parameters)
+            image, other_image = prepare_image_detection(map_, parameters) 
+            nucleus_signal = get_nucleus_signal(image, other_image, parameters)
+            try : # Catch error raised if user enter a spot size too small compare to voxel size
+                parameters, frame_result, spots, clusters, spot_cluster_id = launch_detection(
+                    image,
+                    other_image,
+                    parameters,
+                    cell_label=cytoplasm_label,
+                    nucleus_label=nucleus_label,
+                    hide_loading=True,
+                )
+
+            except ValueError as error :
+                if "The array should have an upper bound of 1" in str(error) :
+                    window_print(batch_window,"Spot size too small for current voxel size.")
+                    continue
+                else :
+                    raise(error)
+
+            if parameters['save detection'] :
+                if parameters['do_cluster_computation'] : 
+                    if len(clusters) > 0 :
+                        spots_list = [spots, clusters[:,:-2]]
+                    else : spots_list = [spots]
+                else : spots_list = [spots]
+                output_spot_tiffvisual(
+                    image,
+                    spots_list= spots_list,
+                    dot_size=2,
+                    path_output= main_dir + "detection/" + file + "_spot_detection.tiff"
+                )
+
+            #4. Spots extraction
+            window_print(batch_window,"Extracting spots : ")
+            if parameters['extract spots'] :
+
+                #Setting parameter for call to lauch spot extraction
+                #Only spots have one file per image to avoir memory overload
+                parameters['do_spots_excel'] = parameters['xlsx']
+                parameters['do_spots_csv'] = parameters['csv']
+                parameters['do_spots_feather'] = parameters['feather']
+                parameters['spots_filename'] = "spots_extractions_{0}".format(file)
+                parameters['spots_extraction_folder'] = main_dir + "results/spots_extraction/"
+
+                launch_spots_extraction(
+                        acquisition_id=acquisition_id + last_acquisition_id,
+                        user_parameters=parameters,
+                        image=image,
+                        spots=spots,
+                        cluster_id=spot_cluster_id,
+                        nucleus_label= nucleus_label,
+                        cell_label= cytoplasm_label,
+                    )
+
+            #5. Features computation
+            window_print(batch_window,"computing features...")
+            new_results_df, new_cell_results_df = launch_features_computation(
+            acquisition_id=acquisition_id + last_acquisition_id,
+            image=image,
+            nucleus_signal = nucleus_signal,
+            spots=spots,
+            clusters=clusters,
+            spots_cluster_id=spot_cluster_id,
+            nucleus_label = nucleus_label,
+            cell_label= cytoplasm_label,
+            user_parameters=parameters,
+            frame_results=frame_result,
+            )
+
+            results_df = pd.concat([
+                results_df.reset_index(drop=True), new_results_df.reset_index(drop=True)
+            ], axis=0)
+
+            cell_results_df = pd.concat([
+                cell_results_df.reset_index(drop=True), new_cell_results_df.reset_index(drop=True)
+            ], axis=0)
+
+
+            #6. Saving results
+            window_print(batch_window,"saving image_results...")
+            #1 file per batch + 1 file per batch if segmentation
+            acquisition_success = write_results(
+                results_df, 
+                path= main_dir + "results/", 
+                filename=batch_name, 
+                do_excel= parameters["xlsx"], 
+                do_feather= parameters["feather"], 
+                do_csv= parameters["csv"],
+                overwrite=True,
+                )
+
+            if do_segmentation :
+                cell_success = write_results(
+                    cell_results_df, 
+                    path= main_dir + "results/", 
+                    filename=batch_name + '_cell_result', 
+                    do_excel= parameters["xlsx"], 
+                    do_feather= parameters["feather"], 
+                    do_csv= parameters["csv"],
+                    overwrite=True,
+                    )
+
+            window_print(batch_window,"Sucessfully saved.")
+
+        except Exception as error :
+            
+            error_count +=1
+            print("Exception raised for acquisition, writting error in error log.")
+
+            log = [
+                f"Error raised during acquisition {acquisition_id}.\n"
+            ]
+            log.append(str(error) + '\n')
+
+            error_log.writelines(log)
+
+            print("Ignoring current acquisition and proceeding to next one.")
+            continue
+
+    
+        
+    batch_progress_bar.update(current_count= acquisition_id+1, max= len(filenames_list))
+    progress_count.update(value=str(acquisition_id+1))
+    batch_window = batch_window.refresh()
+
+    if error_count > 0 :
+        sg.popup(f"Batch processing finished but {error_count} acquisitions were skipped during quantification.\nFor more informations check error_log in result folder.")
+
+    return results_df, cell_results_df, acquisition_id

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/batch/prompt.py

@@ -3,7 +3,7 @@ Submodule with main function to call to launch batch mode.
 """
 
 import os
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 
 from .utils import get_elmt_from_key, create_map, call_auto_map
 from .pipeline import batch_pipeline

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/batch/test.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import small_fish_gui.batch as batch
 import pandas as pd
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/batch/update.py

@@ -1,7 +1,7 @@
 """
 Functions handling GUI update while user is interacting with software.
 """
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 
 from .utils import get_elmt_from_key
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/batch/utils.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 from ..pipeline._preprocess import _auto_map_channels
 from ..pipeline._preprocess import MappingError
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/gui/animation.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import numpy as np
 
 WAITING_TEXT = [

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/gui/help_module.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import os
 
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/gui/layout.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import os
 from ..utils import check_parameter
 import cellpose.models as models

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/gui/napari_visualiser.py

@@ -123,7 +123,7 @@ def __update_clusters(new_clusters: np.ndarray, spots: np.ndarray, voxel_size, c
     Outdated. previous behaviour.
     """
     if len(new_clusters) == 0 : return new_clusters
-    if len(spots) == 0 : return np.empty(shape=(0,2+len(voxel_size)))
+    if len(spots) == 0 : return np.empty(shape=(0,2+len(voxel_size)), dtype=int)
 
     if len(new_clusters[0]) in [2,3] :
         new_clusters = np.concatenate([
@@ -198,7 +198,7 @@ def correct_spots(
         if len(clusters) > 0 :
             clusters_coordinates = clusters[:, :dim]
         else :
-            clusters_coordinates = np.empty(shape=(0,3)) 
+            clusters_coordinates = np.empty(shape=(0,dim), dtype=int) 
         Viewer.add_points( # cluster; this layer can be update by user.
             clusters_coordinates, 
             size = 10, 
@@ -222,14 +222,13 @@ def correct_spots(
     if type(clusters) != type(None) :
         new_clusters = np.round(Viewer.layers['foci'].data).astype(int)
         if len(new_clusters) == 0 :
-            new_clusters = np.empty(shape=(0,5))
-            new_cluster_id = -1 * np.ones(len(new_spots))
+            new_clusters = np.empty(shape=(0,dim + 2), dtype=int)
+            new_cluster_id = -1 * np.ones(shape=(len(new_spots), 1), dtype=int)
             new_spots = np.concatenate([new_spots, new_cluster_id], axis=1)
         else :
             new_cluster_id = Viewer.layers['foci'].features.to_numpy()
             new_clusters = np.concatenate([new_clusters, new_cluster_id], axis=1)
 
-            print("After concatenate new clusters shape = {0}".format(new_clusters.shape))
     
             new_spots, new_clusters = _update_clusters(
                 old_spots =spots,
@@ -243,7 +242,6 @@ def correct_spots(
                 null_value= -2
             )
     
-            print("After _update_cluster\nnew_clusters shape = {0}\nnew_spots shape = {1}".format(new_clusters.shape, new_spots.shape))
 
     else : new_clusters = None
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/gui/prompts.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import pandas as pd
 import os
 import numpy as np

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/interface/inoutput.py

@@ -4,7 +4,7 @@ import numpy as np
 from bigfish.stack import check_parameter
 from typing import Literal
 
-MAX_LEN_EXCEL = 1048576
+MAX_LEN_EXCEL = 1048576 #Maximum number of lines that can be written in an excel file
 
 def _cast_spot_to_tuple(spot) :
     return tuple([coord for coord in spot])
@@ -120,10 +120,21 @@ def input_segmentation(
         nucleus_path : str,
         cytoplasm_path : str,
 ) :
-    nucleus_label = np.load(nucleus_path)
+    
+    if nucleus_path.endswith('.npy') or nucleus_path.endswith('.npz') :
+        nucleus_label = np.load(nucleus_path)
+    else :
+        raise ValueError("Wrong extension for mask file, only npy and npz are supported")
+
 
     if cytoplasm_path != '' :
-        cytoplasm_label = np.load(cytoplasm_path)
+
+        if cytoplasm_path.endswith('.npy') or cytoplasm_path.endswith('.npz') :
+            cytoplasm_label = np.load(cytoplasm_path)
+        else :
+            raise ValueError("Wrong extension for mask file, only npy and npz are supported")
+
+
     else : 
         cytoplasm_label = nucleus_label
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/interface/testing.py

@@ -1,4 +1,4 @@
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 
 layout = [
     [sg.Radio(['A',], key='button', group_id=0, key='test1'),sg.Radio(['B'], key='button', group_id=0, key='test2'), sg.Radio(['C'], key='button', group_id=0, key='test3')],

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/_colocalisation.py

@@ -3,7 +3,7 @@ from ..gui import coloc_prompt, add_default_loading
 
 import numpy as np
 import pandas as pd
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 from scipy.ndimage import distance_transform_edt
 from scipy.signal import fftconvolve
 
@@ -413,7 +413,8 @@ def _cell_coloc(
     colocalisation_df = colocalisation_df.drop('rna_coords', axis=1)
     colocalisation_df['voxel_size'] = [voxel_size]*len(colocalisation_df)
     colocalisation_df['pair_name'] = [(acquisition_name_id1, acquisition_name_id2)] * len(colocalisation_df)
-    colocalisation_df['pair_acquisition_id'] = [(acquisition_id1, acquisition_id2)] * len(colocalisation_df)
+    colocalisation_df['acquisition_id_1'] = [acquisition_id1] * len(colocalisation_df)
+    colocalisation_df['acquisition_id_2'] = [acquisition_id2] * len(colocalisation_df)
     colocalisation_df['colocalisation_distance'] = colocalisation_distance
 
     return colocalisation_df

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/_preprocess.py

@@ -1,6 +1,6 @@
 import numpy as np
 import os
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 from ..gui import _error_popup, _warning_popup, parameters_layout, add_header, prompt, prompt_with_help
 from ..gui.prompts import input_image_prompt
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/actions.py

@@ -25,7 +25,7 @@ from ..hints import pipeline_parameters
 
 import os
 import pandas as pd
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import numpy as np
 
 def segment_cells(user_parameters : pipeline_parameters, nucleus_label, cytoplasm_label) :
@@ -76,6 +76,7 @@ def add_detection(user_parameters : pipeline_parameters, acquisition_id, cytopla
         if type(detection_parameters) != type(None) :
             user_parameters.update(detection_parameters) 
         else : #If user clicks cancel
+            
             cancel = ask_cancel_detection()
             if cancel : 
                 return new_results_df, new_cell_results_df, acquisition_id, user_parameters
@@ -201,13 +202,22 @@ def load_segmentation(nucleus_label, cytoplasm_label, segmentation_done) :
         else :
             return nucleus_label, cytoplasm_label, segmentation_done
 
-    answer = prompt_load_segmentation()
-    if type(answer) == type(None) : #user clicks cancel
-        return nucleus_label, cytoplasm_label, segmentation_done
-    nucleus_label, cytoplasm_label = input_segmentation(
-        answer['nucleus'],
-        answer['cytoplasm'],
-    )
+    while True :
+        answer = prompt_load_segmentation()
+
+        if type(answer) == type(None) : #user clicks cancel
+            return nucleus_label, cytoplasm_label, segmentation_done
+
+        try :
+            nucleus_label, cytoplasm_label = input_segmentation(
+                answer['nucleus'],
+                answer['cytoplasm'],
+            )
+        
+        except ValueError as e :
+            sg.popup(str(e))
+        else :
+            break
 
     if type(nucleus_label) != type(None) and type(nucleus_label) != np.ndarray :
         nucleus_label = nucleus_label['arr_0']

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/detection.py

@@ -19,7 +19,7 @@ from napari.types import LayerDataTuple
 
 import numpy as np
 import pandas as pd
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 from numpy import NaN
 import bigfish.detection as detection
 import bigfish.stack as stack
@@ -183,7 +183,7 @@ def cluster_detection(spots, voxel_size, radius = 350, nb_min_spots = 4, keys_to
     elif isinstance(keys_to_compute, list) : pass
     else : raise TypeError("Wrong type for keys_to_compute. Should be list[str] or str. It is {0}".format(type(keys_to_compute)))
     if len(spots) == 0 :
-        res = {'clustered_spots' : [], 'clusters' : [], 'clustered_spots_dataframe' : pd.DataFrame(columns= ["id", "cluster_id", "z", "y", "x"]), 'clusters_dataframe' : pd.DataFrame(columns= ["id", "z", "y", "x", "spot_number"])}
+        res = {'clustered_spots' : np.empty(shape=(0,len(voxel_size) + 1), dtype=int), 'clusters' : np.empty(shape=(0,len(voxel_size) + 2), dtype=int), 'clustered_spots_dataframe' : pd.DataFrame(columns= ["id", "cluster_id", "z", "y", "x"]), 'clusters_dataframe' : pd.DataFrame(columns= ["id", "z", "y", "x", "spot_number"])}
         return {key : res[key] for key in keys_to_compute}
     else : res = {}
     voxel_size = tuple([int(d) for d in voxel_size])
@@ -192,7 +192,7 @@ def cluster_detection(spots, voxel_size, radius = 350, nb_min_spots = 4, keys_to
 
     if 'clustered_spots' in keys_to_compute :
         res['clustered_spots'] = clustered_spots
-        
+        voxel_size
     if 'clusters' in keys_to_compute : 
         res['clusters'] = clusters
 
@@ -220,7 +220,7 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
             segmentation_done= user_parameters['segmentation_done'],
             default_dict=detection_parameters
             )
-        if type(detection_parameters) == type(None) : return user_parameters
+        if type(detection_parameters) == type(None) : return None
         try :
             detection_parameters = convert_parameters_types(detection_parameters)
             detection_parameters = check_integrity(
@@ -407,9 +407,8 @@ def launch_cell_extraction(
 
     if do_clustering :
         if len(clusters) > 0 :
-
-            free_spots = spots[spots_cluster_id == -1]
-            clustered_spots = spots[spots_cluster_id != -1]
+            free_spots = spots[spots_cluster_id == -1].astype(int)
+            clustered_spots = spots[spots_cluster_id != -1].astype(int)
 
             other_coords = {
                 'clusters_coords' : clusters,
@@ -471,6 +470,13 @@ def launch_cell_extraction(
         free_spots_coords = cell.get('free_spots')
         signal = cell['image']
 
+        if do_clustering :
+            if len(clusters) > 0 :
+                compute_foci = True
+            else : 
+                compute_foci = False
+        else : compute_foci = False
+
         with np.errstate(divide= 'ignore', invalid= 'ignore') :
             features = classification.compute_features(
                 cell_mask=cell_mask,
@@ -485,7 +491,7 @@ def launch_cell_extraction(
                 compute_area=True,
                 compute_dispersion=True,
                 compute_distance=True,
-                compute_foci= do_clustering and len(clusters) > 0,
+                compute_foci= compute_foci,
                 compute_intranuclear=True,
                 compute_protrusion=False,
                 compute_topography=True
@@ -535,7 +541,8 @@ def launch_cell_extraction(
 
         features = [acquisition_id, cell_id, cell_bbox] + features
         features += [rna_coords, foci_coords, clustered_spots_coords, free_spots_coords]
-        features += [len(clustered_spots_coords), len(free_spots_coords)]
+        features += [len(clustered_spots_coords) if type(clustered_spots_coords) != type(None) else None]
+        features += [len(free_spots_coords) if type(free_spots_coords) != type(None) else None]
         
         result_frame = pd.concat([
             result_frame,
@@ -703,7 +710,14 @@ def launch_features_computation(
     if user_parameters['segmentation_done'] : 
         cell_result_dframe['name'] = name
         cell_result_dframe = cell_result_dframe.loc[:,['name'] + cell_result_col]
-        cell_result_dframe['total_rna_number'] = cell_result_dframe['nb_rna_in_nuc'] + cell_result_dframe['nb_rna_out_nuc']
+        if 'nb_rna_in_nuc' in cell_result_dframe.columns and 'nb_rna_out_nuc' in cell_result_dframe.columns :
+            cell_result_dframe['total_rna_number'] = cell_result_dframe['nb_rna_in_nuc'] + cell_result_dframe['nb_rna_out_nuc']
+        else : # This can happen when segmentation is performed and detects cells but they are on fov edges and thus removed by big-fish.
+            print("\033[1;31m All segmented cells where skipped because they are found on fov edges (incomplete cells), if you want to analyse this image check segmentation.\033[00m")
+            cell_result_dframe['nb_rna_in_nuc'] = np.NaN
+            cell_result_dframe['nb_rna_out_nuc'] = np.NaN
+            cell_result_dframe['total_rna_number'] = np.NaN
+
         
     return frame_results, cell_result_dframe
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/main.py

@@ -3,7 +3,7 @@ This script is called when software starts; it is the main loop.
 """
 
 import pandas as pd
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 from ..gui import hub_prompt
 from .actions import add_detection, save_results, compute_colocalisation, delete_acquisitions, rename_acquisitions, save_segmentation, load_segmentation, segment_cells
 from ._preprocess import clean_unused_parameters_cache

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/segmentation.py

@@ -20,7 +20,7 @@ import numpy as np
 import bigfish.multistack as multistack
 import bigfish.stack as stack
 import bigfish.plot as plot
-import PySimpleGUI as sg
+import FreeSimpleGUI as sg
 import matplotlib.pyplot as plt
 import os
 

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/pipeline/testing.ipynb

@@ -2045,7 +2045,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "cellpose",
+   "display_name": "small_fish",
    "language": "python",
    "name": "python3"
   },
@@ -2059,7 +2059,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "version": "3.8.19"
   }
  },
  "nbformat": 4,

{small_fish_gui-1.9.1 → small_fish_gui-1.9.3}/src/small_fish_gui/requirements.txt

@@ -9,7 +9,7 @@ napari-plugin-manager==0.1.0a2
 napari-svg==0.1.10
 numpy==1.24.4
 pandas==1.5.3
-PySimpleGUI==4.60.5
+FreeSimpleGUI==5.1.1
 scipy==1.9.1
 scikit-image==0.19.1
 scikit-learn==1.3.2

small_fish_gui-1.9.1/src/small_fish_gui/.readthedocs.yaml

@@ -1,21 +0,0 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See for details
-
-# Required
-version: 2
-
-# Set the OS, Python version and other tools you might need
-build:
-  os: ubuntu-22.04
-  tools:
-    python: "3.8"
-
-# Build documentation in the "docs/" directory with Sphinx
-sphinx:
-  configuration: docs/conf.py
-
-# Optionally build your docs in additional formats such as PDF and ePub
-formats:
-   - pdf
-   - epub

small_fish_gui-1.9.1/src/small_fish_gui/batch/pipeline.py

@@ -1,228 +0,0 @@
-"""
-Submodule keeping necessary calls from main pipeline for batch processing.
-"""
-
-import os
-import pandas as pd
-import PySimpleGUI as sg
-
-from ..hints import pipeline_parameters
-
-from .input import open_image
-from ..interface import write_results
-from ..pipeline import reorder_shape, reorder_image_stack, prepare_image_detection
-from ..pipeline import cell_segmentation, launch_detection, launch_features_computation
-from ..pipeline import launch_spots_extraction
-from ..pipeline import get_nucleus_signal
-from ..pipeline import _cast_segmentation_parameters, convert_parameters_types
-from ..pipeline import plot_segmentation, output_spot_tiffvisual
-from ..utils import get_datetime
-
-def window_print(window: sg.Window, *args) :
-    print(*args)
-    window.refresh()
-
-def batch_pipeline(
-        batch_window : sg.Window,
-        batch_progress_bar : sg.ProgressBar,
-        progress_count : sg.Text,
-        parameters : pipeline_parameters,
-        filenames_list : list,
-        do_segmentation : bool,
-        map_ : dict,
-        results_df : pd.DataFrame,
-        cell_results_df : pd.DataFrame,
-        is_3D,
-        last_acquisition_id=0,
-) :
-    
-    #Extracting parameters
-    input_path = parameters['Batch_folder']
-    output_path = parameters['output_folder']
-    batch_name = parameters['batch_name']
-    time = '_' + get_datetime()
-
-    #Preparing folder
-    window_print(batch_window,"Creating folders for output...")
-    main_dir = output_path + "/" + batch_name + time + "/"
-    os.makedirs(main_dir + "results/", exist_ok=True)
-    if parameters['save segmentation'] : os.makedirs(main_dir + "segmentation/", exist_ok=True)
-    if parameters['save detection'] : os.makedirs(main_dir + "detection/", exist_ok=True)
-    if parameters['extract spots'] : os.makedirs(main_dir + "results/spots_extraction", exist_ok=True)
-
-    #Setting spot detection dimension
-    parameters['dim'] = 3 if is_3D else 2
-
-    #Pipeline loop
-    window_print(batch_window,"Launching batch analysis...")
-    batch_progress_bar.update(max=len(filenames_list))
-    filenames_list.sort()
-    for acquisition_id, file in enumerate(filenames_list) :
-        
-        #GUI
-        window_print(batch_window,"\nNext file : {0}".format(file))
-        batch_progress_bar.update(current_count= acquisition_id, max= len(filenames_list))
-        progress_count.update(value=str(acquisition_id))
-        batch_window = batch_window.refresh()
-        
-        #0. Open image
-        image = open_image(input_path + '/' + file)
-        parameters['image'] = image
-        parameters['filename'] = file
-        for key_to_clean in [0,2] : 
-            if key_to_clean in parameters : del parameters[key_to_clean]
-
-        #1. Re-order shape
-        shape = image.shape
-        parameters['shape'] = shape
-        parameters['reordered_shape'] = reorder_shape(shape, map_=map_)
-
-        #2. Segmentation (opt)
-        if do_segmentation :
-            window_print(batch_window,"Segmenting cells...")
-            im_seg = reorder_image_stack(map_, image)
-            parameters = _cast_segmentation_parameters(parameters)
-            cytoplasm_label, nucleus_label = cell_segmentation(
-                im_seg,
-                cyto_model_name= parameters['cyto_model_name'],
-                cyto_diameter= parameters['cytoplasm diameter'],
-                nucleus_model_name= parameters['nucleus_model_name'],
-                nucleus_diameter= parameters['nucleus diameter'],
-                channels=[parameters['cytoplasm channel'], parameters['nucleus channel']],
-                do_only_nuc=parameters['Segment only nuclei']
-                )
-            
-            parameters['segmentation_done'] = True
-
-            if cytoplasm_label.max() == 0 : #No cell segmented
-                window_print(batch_window,"No cell was segmented, computing next image.")
-                continue
-            else : 
-                window_print(batch_window, "{0} cells segmented.".format(cytoplasm_label.max()))
-
-                if parameters['save segmentation'] :
-                    plot_segmentation(
-                        cyto_image=im_seg[parameters['cytoplasm channel']],
-                        cyto_label= cytoplasm_label,
-                        nuc_image= im_seg[parameters['nucleus channel']],
-                        nuc_label=nucleus_label,
-                        path= main_dir + "segmentation/" + file,
-                        do_only_nuc= parameters['Segment only nuclei'],
-                    )
-
-        else :
-            cytoplasm_label, nucleus_label = None,None
-            parameters['segmentation_done'] = False
-
-        #3. Detection, deconvolution, clusterisation
-        window_print(batch_window,"Detecting spots...")
-        parameters = convert_parameters_types(parameters)
-        image, other_image = prepare_image_detection(map_, parameters) 
-        nucleus_signal = get_nucleus_signal(image, other_image, parameters)
-        try : # Catch error raised if user enter a spot size too small compare to voxel size
-            parameters, frame_result, spots, clusters, spot_cluster_id = launch_detection(
-                image,
-                other_image,
-                parameters,
-                cell_label=cytoplasm_label,
-                nucleus_label=nucleus_label,
-                hide_loading=True,
-            )
-
-        except ValueError as error :
-            if "The array should have an upper bound of 1" in str(error) :
-                window_print(batch_window,"Spot size too small for current voxel size.")
-                continue
-            else :
-                raise(error)
-        
-        if parameters['save detection'] :
-            if parameters['do_cluster_computation'] : 
-                if len(clusters) > 0 :
-                    spots_list = [spots, clusters[:,:-2]]
-                else : spots_list = [spots]
-            else : spots_list = [spots]
-            output_spot_tiffvisual(
-                image,
-                spots_list= spots_list,
-                dot_size=2,
-                path_output= main_dir + "detection/" + file + "_spot_detection.tiff"
-            )
-
-        #4. Spots extraction
-        window_print(batch_window,"Extracting spots : ")
-        if parameters['extract spots'] :
-
-            #Setting parameter for call to lauch spot extraction
-            #Only spots have one file per image to avoir memory overload
-            parameters['do_spots_excel'] = parameters['xlsx']
-            parameters['do_spots_csv'] = parameters['csv']
-            parameters['do_spots_feather'] = parameters['feather']
-            parameters['spots_filename'] = "spots_extractions_{0}".format(file)
-            parameters['spots_extraction_folder'] = main_dir + "results/spots_extraction/"
-
-            launch_spots_extraction(
-                    acquisition_id=acquisition_id + last_acquisition_id,
-                    user_parameters=parameters,
-                    image=image,
-                    spots=spots,
-                    cluster_id=spot_cluster_id,
-                    nucleus_label= nucleus_label,
-                    cell_label= cytoplasm_label,
-                )
-
-        #5. Features computation
-        window_print(batch_window,"computing features...")
-        new_results_df, new_cell_results_df = launch_features_computation(
-        acquisition_id=acquisition_id + last_acquisition_id,
-        image=image,
-        nucleus_signal = nucleus_signal,
-        spots=spots,
-        clusters=clusters,
-        spots_cluster_id=spot_cluster_id,
-        nucleus_label = nucleus_label,
-        cell_label= cytoplasm_label,
-        user_parameters=parameters,
-        frame_results=frame_result,
-        )
-
-        results_df = pd.concat([
-            results_df.reset_index(drop=True), new_results_df.reset_index(drop=True)
-        ], axis=0)
-
-        cell_results_df = pd.concat([
-            cell_results_df.reset_index(drop=True), new_cell_results_df.reset_index(drop=True)
-        ], axis=0)
-
-
-        #6. Saving results
-        window_print(batch_window,"saving image_results...")
-        #1 file per batch + 1 file per batch if segmentation
-        acquisition_success = write_results(
-            results_df, 
-            path= main_dir + "results/", 
-            filename=batch_name, 
-            do_excel= parameters["xlsx"], 
-            do_feather= parameters["feather"], 
-            do_csv= parameters["csv"],
-            overwrite=True,
-            )
-        
-        if do_segmentation :
-            cell_success = write_results(
-                cell_results_df, 
-                path= main_dir + "results/", 
-                filename=batch_name + '_cell_result', 
-                do_excel= parameters["xlsx"], 
-                do_feather= parameters["feather"], 
-                do_csv= parameters["csv"],
-                overwrite=True,
-                )
-        
-        window_print(batch_window,"Sucessfully saved.")
-
-        
-    batch_progress_bar.update(current_count= acquisition_id+1, max= len(filenames_list))
-    progress_count.update(value=str(acquisition_id+1))
-    batch_window = batch_window.refresh()
-    return results_df, cell_results_df, acquisition_id