small-fish-gui 1.9.2__tar.gz → 1.9.4__tar.gz

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/PKG-INFO

@@ -1,8 +1,9 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.2
+Version: 1.9.4
 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: Wiki, https://github.com/2Echoes/small_fish_gui/wiki
 Project-URL: Issues, https://github.com/2Echoes/small_fish/issues
 Author-email: Slimani Floric <floric.slimani@live.com>
 License-File: LICENSE
@@ -13,6 +14,7 @@ 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 +25,6 @@ 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-1.9.2 → small_fish_gui-1.9.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.9.2"
+version = "1.9.4"
 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",
@@ -38,4 +38,5 @@ dependencies = [
 
 [project.urls]
 Homepage = "https://github.com/2Echoes/small_fish"
+Wiki = "https://github.com/2Echoes/small_fish_gui/wiki"
 Issues = "https://github.com/2Echoes/small_fish/issues"

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/src/small_fish_gui/README.md

@@ -5,7 +5,7 @@ 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 +93,12 @@ Note that for training it is recommended to first set up your GPU as training co
 ## Developpement
 
 Optional features to include in future versions : 
-- time stack (which would include cell tracking)
-- 3D segmentation
+
+**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
+* In Napari viewer, or add an extra spot layer to visualsize spots that are in foci or color spots that are in clusters in specific color.

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/src/small_fish_gui/__init__.py

@@ -36,6 +36,5 @@ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
 ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-
 """
-__version__ = "1.9.2"
+__version__ = "1.9.4"

small_fish_gui-1.9.4/src/small_fish_gui/__main__.py

@@ -0,0 +1,62 @@
+import sys, subprocess, traceback, os, re
+from small_fish_gui import __version__
+
+def main():
+    import small_fish_gui.pipeline.main
+
+def _get_version() :
+    return __version__
+
+AVAILABLE_ARGUMENTS = {
+    ('-v','--v','--version') : "Prompt the software version.",
+    ('--launch', '-l') : "Launch small fish gui, equivalent to no arguments.",
+    ('-h', '--help', '--h') : "Prompt this help menu."
+}
+
+def is_last_version() :
+    
+    query = subprocess.run([sys.executable, '-m', 'pip', 'index', 'versions', 'small_fish_gui'], capture_output=True, text=True)
+    all_version = query.stdout.split(',')
+    latest_version = all_version[0]
+    regex = r"\d+\.\d+\.\d+"
+    latest = re.findall(regex, latest_version)
+    
+    current_version = _get_version()
+    
+    if len(latest) == 0 : 
+        return current_version
+    else :
+        return current_version == latest[-1]
+
+if __name__ == "__main__":
+
+    if not is_last_version() :
+        print("A new version of Small Fish is available. To update close small fish and type :\npip install --upgrade small_fish_gui")
+
+    try :
+        arguments = sys.argv
+
+        if len(arguments) > 1 :
+            if arguments[1] in ['-v','--v','--version'] :
+                print(_get_version())
+                quit()
+            elif arguments[1] in ['--launch', '-l'] :
+                pass
+            elif arguments[1] in ['-h', '--help', '--h'] :
+                for key, help in AVAILABLE_ARGUMENTS.items() :
+                    print(f"{key} : {help}")
+                quit()
+            else :
+                print(f"Incorrect argument : {arguments}, to launch small fish don't pass any argument or pick amongst {AVAILABLE_ARGUMENTS.keys()}")
+
+        sys.exit(main())
+
+    except Exception as error :
+        with open("error_log.txt",'a') as error_log :
+            error_log.writelines([
+                f"version {_get_version()}",
+                f"error : {error}",
+                f"traceback :\n{traceback.format_exc()}",
+            ])
+
+        print(f"error_log saved at {os.getcwd()}/error_log.txt. Please consider reporting this by opening an issue on github.")

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/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-1.9.4/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/src/small_fish_gui/gui/__init__.py

@@ -15,6 +15,7 @@ from .prompts import ask_cancel_detection
 from .prompts import ask_cancel_segmentation
 from .prompts import ask_help
 from .prompts import ask_detection_confirmation
+from .prompts import prompt_restore_main_menu
 
 #Helpers to build windows
 from .layout import parameters_layout 

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/src/small_fish_gui/gui/napari_visualiser.py

@@ -198,7 +198,7 @@ def correct_spots(
         if len(clusters) > 0 :
             clusters_coordinates = clusters[:, :dim]
         else :
-            clusters_coordinates = np.empty(shape=(0,3), dtype=int) 
+            clusters_coordinates = np.empty(shape=(0,dim), dtype=int) 
         Viewer.add_points( # cluster; this layer can be update by user.
             clusters_coordinates, 
             size = 10, 
@@ -222,8 +222,8 @@ 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), dtype=int)
-            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()

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/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
@@ -222,7 +222,6 @@ def detection_parameters_promt(
     else : values['dim'] = 2
     return values
 
-
 def ask_replace_file(filename:str) :
     layout = [
         [sg.Text("{0} already exists, replace ?")],
@@ -341,7 +340,6 @@ def ask_cancel_detection() :
     else :
         return True
 
-
 def ask_confirmation(question_displayed : str) :
     layout =[
         [sg.Text(question_displayed, font= 'bold 10')],
@@ -355,7 +353,6 @@ def ask_confirmation(question_displayed : str) :
     else :
         return True
     
-
 def prompt_save_segmentation() -> 'dict[Literal["folder","filename","ext"]]':
     while True :
         relaunch = False
@@ -406,4 +403,29 @@ def prompt_load_segmentation() -> 'dict[Literal["nucleus","cytoplasm"]]':
         if not relaunch : break
 
 
-    return values
+    return values
+
+def prompt_restore_main_menu() -> bool :
+    """
+    Warn user that software will try to go back to main menu while saving parameters, and propose to save results and quit if stuck.
+
+    Returns True if user want to save and quit else False, to raise error close window.
+    """
+
+
+    layout = [
+        [sg.Text("An error was caught while proceeding.\nSoftware can try to save parameters and return to main menu or save results and quit.")],
+        [sg.Button("Return to main menu", key='menu'), sg.Button("Save and quit", key='save')]
+    ]
+
+    window = sg.Window('small fish', layout=layout, margins=(10,10), auto_size_text=True, resizable=True)
+    event, values = window.read(close=True)
+
+    if event is None :
+        return None
+    elif event == "save" :
+        return True
+    elif event == "menu" :
+        return False
+    else :
+        raise AssertionError("Unforseen answer")

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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
@@ -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(
@@ -710,7 +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-1.9.2 → small_fish_gui-1.9.4}/src/small_fish_gui/pipeline/main.py

@@ -2,9 +2,10 @@
 This script is called when software starts; it is the main loop.
 """
 
+import traceback
 import pandas as pd
-import PySimpleGUI as sg
-from ..gui import hub_prompt
+import FreeSimpleGUI as sg
+from ..gui import hub_prompt, prompt_restore_main_menu
 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
 from ..batch import batch_promp
@@ -109,5 +110,21 @@ while True : #Break this loop to close small_fish
 
     except Exception as error :
         sg.popup(str(error))
-        raise error
+
+        save_quit = prompt_restore_main_menu()
+
+        if save_quit is None :
+            raise error
+
+        elif save_quit :
+            save_results(
+                result_df=result_df,
+                cell_result_df=cell_result_df,
+                global_coloc_df=global_coloc_df,
+                cell_coloc_df = cell_coloc_df,
+            )
+            quit()
+        else :
+            continue
+
 quit()

{small_fish_gui-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2 → small_fish_gui-1.9.4}/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-1.9.2/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-1.9.2/src/small_fish_gui/__main__.py

@@ -1,29 +0,0 @@
-import sys, subprocess
-import PySimpleGUI as sg
-
-from small_fish_gui import __version__
-
-def main():
-    import small_fish_gui.pipeline.main
-
-def is_last_version() :
-    latest_version = str(subprocess.run([sys.executable, '-m', 'pip', 'install', '{}==random'.format('small_fish_gui')], capture_output=True, text=True))
-    latest_version = latest_version[latest_version.find('(from versions:')+15:]
-    latest_version = latest_version[:latest_version.find(')')]
-    latest_version = latest_version.replace(' ','').split(',')[-1]
-
-    current_version = __version__
-
-    return current_version == latest_version
-
-if __name__ == "__main__":
-
-    if not is_last_version() :
-        print("A new version of Small Fish is available. To update close small fish and type :\npip install --upgrade small_fish_gui")
-
-    try :
-        sys.exit(main())
-    except Exception as error :
-        sg.popup("Sorry. Something went wrong...\nIf you have some time to spare could you please communicate the error you encountered (next window) on :\nhttps://github.com/2Echoes/small_fish/issues.")
-        sg.popup_error_with_traceback(error)
-        raise error

small_fish_gui-1.9.2/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