small-fish-gui 1.10.2__tar.gz → 1.10.4__tar.gz

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.10.2
+Version: 1.10.4
 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
@@ -12,6 +12,7 @@ Classifier: Operating System :: OS Independent
 Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.9
 Requires-Dist: aicsimageio>=4.14.0
+Requires-Dist: aicspylibczi==3.3.1
 Requires-Dist: big-fish==0.6.2
 Requires-Dist: cellpose==3.0.7
 Requires-Dist: czifile==2019.7.2

small_fish_gui-1.10.4/error_log.txt

@@ -0,0 +1,9 @@
+version 1.10.3error : 'voxel_size_z'traceback :
+Traceback (most recent call last):
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/main.py", line 40, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/actions.py", line 75, in add_detection
+    detection_parameters = initiate_detection(
+  File "/home/floric/miniconda3/envs/dev/lib/python3.9/site-packages/small_fish_gui/pipeline/detection.py", line 227, in initiate_detection
+    detection_parameters['spot_size_z'] = round(detection_parameters['voxel_size_z']*1.5) if isinstance(detection_parameters['voxel_size_z'], (float,int)) else None
+KeyError: 'voxel_size_z'

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "1.10.2"
+version = "1.10.4"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.com" },
 ]
@@ -35,7 +35,7 @@ dependencies = [
 "openpyxl==3.1.2",
 "pyarrow==11.0.0",
 "aicsimageio>=4.14.0",
-
+"aicspylibczi==3.3.1",
 ]
 
 [project.urls]

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/__init__.py

@@ -37,7 +37,7 @@ 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__ = "1.10.2"
+__version__ = "1.10.4"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/batch/integrity.py

@@ -8,6 +8,7 @@ import bigfish.stack as stack
 import numpy as np
 import FreeSimpleGUI as sg
 
+from ..hints import pipeline_parameters
 from ..pipeline._preprocess import check_integrity, convert_parameters_types, ParameterInputError, _check_segmentation_parameters
 from ..pipeline.segmentation import _cast_segmentation_parameters
 
@@ -100,7 +101,7 @@ def check_segmentation_parameters(
     return segmentation_is_ok, values
 
 def check_detection_parameters(
-        values,
+        values : pipeline_parameters,
         do_dense_region_deconvolution,
         do_clustering,
         is_multichannel,
@@ -117,7 +118,7 @@ def check_detection_parameters(
             do_dense_region_deconvolution=do_dense_region_deconvolution,
             do_clustering=do_clustering,
             multichannel=is_multichannel,
-            segmentation_done=None,
+            segmentation_done= values['do_segmentation'],
             map_=map_,
             shape=shape
         )

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/batch/pipeline.py

@@ -49,6 +49,9 @@ def batch_pipeline(
     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)
+    first_save = True # init for excel append
+    append_to_line = 1 #Start at line one
+    cell_append_to_line = 1 #Start at line one
 
     #Setting spot detection dimension
     parameters['dim'] = 3 if is_3D else 2
@@ -62,6 +65,12 @@ def batch_pipeline(
     error_log = open(main_dir + "error_log", mode='w')
     error_count = 0
 
+    #These columns usually kept for coloc analysis will be dropped for memory gain in batch mode
+    COLUMNS_TO_DROP = ['image', 'spots', 'clusters', 'rna_coords', 'cluster_coords',"rna_coords", "cluster_coords", "free_spots_coords", "clustered_spots_coords"]
+    for col in COLUMNS_TO_DROP :
+                if col in cell_results_df : cell_results_df.drop(columns=col)
+                if col in results_df : results_df.drop(columns=col)
+
     for acquisition_id, file in enumerate(filenames_list) :
         try :
 
@@ -192,6 +201,10 @@ def batch_pipeline(
             frame_results=frame_result,
             )
 
+            for col in COLUMNS_TO_DROP :
+                if col in new_cell_results_df : new_cell_results_df.drop(columns=col)
+                if col in new_results_df : new_results_df.drop(columns=col)
+
             results_df = pd.concat([
                 results_df.reset_index(drop=True), new_results_df.reset_index(drop=True)
             ], axis=0)
@@ -202,6 +215,10 @@ def batch_pipeline(
 
 
             #6. Saving results
+            if parameters['xlsx'] :
+                if first_save : xlsx_header = True
+                else : xlsx_header = False
+
             window_print(batch_window,"saving image_results...")
             #1 file per batch + 1 file per batch if segmentation
             acquisition_success = write_results(
@@ -212,7 +229,12 @@ def batch_pipeline(
                 do_feather= parameters["feather"], 
                 do_csv= parameters["csv"],
                 overwrite=True,
+                batch_mode=True,
+                header=first_save,
+                xlsx_start_line=append_to_line
                 )
+            append_to_line += len(results_df)
+            results_df = results_df.drop(results_df.index)
 
             if do_segmentation :
                 cell_success = write_results(
@@ -223,10 +245,16 @@ def batch_pipeline(
                     do_feather= parameters["feather"], 
                     do_csv= parameters["csv"],
                     overwrite=True,
+                    batch_mode=True,
+                    header=first_save,
+                    xlsx_start_line=cell_append_to_line
                     )
-
+                cell_append_to_line += len(cell_results_df)
+                cell_results_df = cell_results_df.drop(cell_results_df.index)
+            first_save = False
             window_print(batch_window,"Sucessfully saved.")
 
+
         except Exception as error :
             
             error_count +=1

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/gui/_napari_widgets.py

@@ -56,7 +56,7 @@ class ClusterWizard(ABC) :
 CLUSTER_WIZARDS = []
 def register_cluster_wizard(cls):
     """
-    Helper to register all clusters related class
+    Helper to register all clusters related wizard class. Object to be instanciated upon launching napari but that have no widget.
     """
     CLUSTER_WIZARDS.append(cls)
     return cls
@@ -198,6 +198,8 @@ class ClusterIDSetter(ClusterWidget) :
                     new_spot_number = len(self.single_layer.features.loc[self.single_layer.features['cluster_id'] == cluster_id])
                     self.cluster_layer.features.loc[self.cluster_layer.features['cluster_id'] == cluster_id, ["spot_number"]] = new_spot_number
                 self.cluster_layer.events.features()
+            else :
+                print(f"Not cluster with id {cluster_id} was found.")
 
             self.cluster_layer.selected_data.clear()
 
@@ -490,7 +492,6 @@ class ClusterCleaner(ClusterWizard) :
 
         def delete_empty_cluster() :
             drop_idx = self.cluster_layer.features[self.cluster_layer.features['spot_number'] == 0].index
-            print("drop_idx : ",drop_idx)
             
             if len(drop_idx) > 0 :
                 print("Removing {} empty cluster(s)".format(len(drop_idx)))

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/interface/inoutput.py

@@ -71,7 +71,20 @@ def write_list_of_results(
     return True
 
 
-def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= True, do_feather= False, do_csv=False, overwrite=False, reset_index=True) :
+def write_results(
+        dataframe: pd.DataFrame, 
+        path:str, 
+        filename:str, 
+        do_excel= True, 
+        do_feather= False, 
+        do_csv=False, 
+        overwrite=False, 
+        reset_index=True, 
+        batch_mode = False,
+        header = True,
+        xlsx_start_line = 1,
+        ) :
+    
     check_parameter(dataframe= pd.DataFrame, path= str, filename = str, do_excel = bool, do_feather = bool)
 
     if len(dataframe) == 0 : return True
@@ -103,16 +116,20 @@ def write_results(dataframe: pd.DataFrame, path:str, filename:str, do_excel= Tru
 
     if reset_index : dataframe = dataframe.reset_index(drop=True)
 
-    if do_csv : dataframe.to_csv(path + new_filename + '.csv', sep=";")
+    if do_csv : 
+        if batch_mode : mode = 'a'
+        else : mode = 'w'
+        dataframe.to_csv(path + new_filename + '.csv', sep=";", header=header, mode=mode)
     if do_excel : 
         if len(dataframe) < MAX_LEN_EXCEL :
-            dataframe.to_excel(path + new_filename + '.xlsx')
+            dataframe.to_excel(path + new_filename + '.xlsx', header=header, startrow=xlsx_start_line)
         else : 
             print("Error : Table too big to be saved in excel format.")
             return False
     
-    if do_feather : 
-        dataframe.to_parquet(path + new_filename + '.parquet')
+    if do_feather :
+        print("feather saving is depreciated, please use csv instead") 
+        pass
 
     return True
 

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/pipeline/detection.py

@@ -218,9 +218,9 @@ def initiate_detection(user_parameters : pipeline_parameters, map_, shape) :
         pass
     else :
         detection_parameters['voxel_size'] = [round(v) if isinstance(v, (float,int)) else None for v in voxel_size]
-        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0]
-        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1]
-        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2]
+        detection_parameters['voxel_size_z'] = detection_parameters['voxel_size'][0] if isinstance(detection_parameters['voxel_size'][0], (float,int)) else None
+        detection_parameters['voxel_size_y'] = detection_parameters['voxel_size'][1] if isinstance(detection_parameters['voxel_size'][1], (float,int)) else None
+        detection_parameters['voxel_size_x'] = detection_parameters['voxel_size'][2] if isinstance(detection_parameters['voxel_size'][2], (float,int)) else None
 
     #Setting default spot size to 1.5 voxel
     if detection_parameters.get('spot_size') is None :

{small_fish_gui-1.10.2 → small_fish_gui-1.10.4}/src/small_fish_gui/requirements.txt

@@ -15,4 +15,5 @@ scikit-image==0.19.1
 scikit-learn==1.3.2
 openpyxl>=3.1.2
 pyarrow>=11.0.0
-aicsimageio>=aicsimageio==4.14.0
+aicsimageio>=aicsimageio==4.14.0
+aicspylibczi==3.3.1