small-fish-gui 2.1.1__py3-none-any.whl → 2.1.3__py3-none-any.whl

small_fish_gui/pipeline/_colocalisation.py

@@ -137,7 +137,11 @@ def spots_colocalisation(
         voxel_size : (z,y,x) tuple
     """
 
+    #No cluster or no spots case
+    if spot_list1 is np.nan or spot_list2 is np.nan : return np.nan
     if len(spot_list1) == 0 or len(spot_list2) == 0 : return np.nan
+    
+    #Dim check
     if len(spot_list1[0]) != len(spot_list2[0]) : 
         raise MissMatchError("dimensionalities of spots 1 and spots 2 don't match.")
 
@@ -170,7 +174,10 @@ def initiate_colocalisation(
         ) :
 
     result_tables = result_tables.set_index('acquisition_id', drop=False)
-    available_spots = dict(zip(result_tables['acquisition_id'].astype(str).str.cat(result_tables['name'],sep='-'), result_tables.index))
+    if len(result_tables) != 0 :
+        available_spots = dict(zip(result_tables['acquisition_id'].astype(str).str.cat(result_tables['name'],sep='-'), result_tables.index))
+    else :
+        available_spots = {}
     default_values = dict(get_settings())
 
     while True :
@@ -228,7 +235,7 @@ def _global_coloc(acquisition_id1,acquisition_id2, result_dataframe, colocalisat
     assert len(acquisition1) == 1
     assert len(acquisition2) == 1
 
-    acquisition_couple = (acquisition_id1,acquisition_id2)
+    acquisition_couple = (int(acquisition_id1),int(acquisition_id2))
 
     voxel_size1 = acquisition1.iloc[0].at['voxel_size']
     voxel_size2 = acquisition2.iloc[0].at['voxel_size']
@@ -352,6 +359,7 @@ def _cell_coloc(
     pivot_values_columns = ['rna_coords', 'total_rna_number']
     if 'clusters' in acquisition2.columns or 'clusters' in acquisition1.columns:
         pivot_values_columns.extend(['clustered_spots_coords','clustered_spot_number'])
+        print(cell_dataframe.loc[:,["clustered_spots_coords"]])
     cell_dataframe.loc[:,['cell_id']] = cell_dataframe['cell_id'].astype(int)
     colocalisation_df = cell_dataframe.pivot(
         columns=['name', 'acquisition_id'],
@@ -380,7 +388,9 @@ def _cell_coloc(
     colocalisation_df[("spots_with_spots_fraction",coloc_name_backward,"backward")] = colocalisation_df[("spots_with_spots_count",coloc_name_backward,"backward")].astype(float) / colocalisation_df[('total_rna_number',acquisition_name_id2,acquisition_id2)].astype(float)
 
     if 'clusters' in acquisition2.columns:
-        if len(acquisition2['clusters'].iat[0]) > 0 :
+        if len(acquisition2['clusters'].iat[0]) > 0  or len(acquisition2['clustered_spots_coords'][acquisition2['clustered_spots_coords'] != -1]) > 0 :
+            
+            print("COLOCALISATION_DF\n", colocalisation_df.loc[:,('clustered_spots_coords',acquisition_name_id2,acquisition_id2)])
 
             #spots to clusters
             colocalisation_df[("spots_with_clustered_spots_count",coloc_name_forward,"forward")] = colocalisation_df.apply(

small_fish_gui/pipeline/actions.py

@@ -30,6 +30,7 @@ from ..hints import pipeline_parameters
 from ..__init__ import __wiki__
 
 import os
+import traceback
 import pandas as pd
 import FreeSimpleGUI as sg
 import numpy as np
@@ -302,61 +303,74 @@ def compute_colocalisation(
         return global_coloc_df, cell_coloc_df, max_id
 
     if os.path.isfile(spots1_key) :
-        Spots1 = load_spots(spots1_key)
-        fake_acquisition = reconstruct_acquisition_data(
-            Spots=Spots1,
-            max_id=max_id,
-            filename= os.path.basename(spots1_key),
-            voxel_size = voxel_size
-        )
-        result_dataframe = pd.concat([
-            result_dataframe,
-            fake_acquisition
-        ], axis=0)
-
-        if not Spots1['cell_label'].isna().all() :
-            fake_cells = reconstruct_cell_data(
+        try :
+            Spots1 = load_spots(spots1_key)
+            fake_acquisition = reconstruct_acquisition_data(
                 Spots=Spots1,
                 max_id=max_id,
+                filename= os.path.basename(spots1_key),
+                voxel_size = voxel_size
             )
-
-            cell_result_dataframe = pd.concat([
-                cell_result_dataframe,
-                fake_cells
+            result_dataframe = pd.concat([
+                result_dataframe,
+                fake_acquisition
             ], axis=0)
 
-        max_id +=1
-        acquisition_id1 = fake_acquisition.iloc[0].at['acquisition_id']
+            if not Spots1['cell_label'].isna().all() :
+                fake_cells = reconstruct_cell_data(
+                    Spots=Spots1,
+                    max_id=max_id,
+                    filename= os.path.basename(spots1_key)
+                )
+
+                cell_result_dataframe = pd.concat([
+                    cell_result_dataframe,
+                    fake_cells
+                ], axis=0)
+
+            max_id +=1
+            acquisition_id1 = fake_acquisition.iloc[0].at['acquisition_id']
+        except ValueError as e :
+            sg.popup("Could not reconstruct coordinates from selected file (Spots 1)")
+            traceback.print_exception(e)
+            return global_coloc_df, cell_coloc_df, max_id
+        
 
     else :
         acquisition_id1 = spots1_key
     
     if os.path.isfile(spots2_key) :
-        Spots2 = load_spots(spots2_key)
-        fake_acquisition = reconstruct_acquisition_data(
-            Spots=Spots2,
-            max_id=max_id,
-            filename= os.path.basename(spots2_key),
-            voxel_size = voxel_size
-        )
-        result_dataframe = pd.concat([
-            result_dataframe,
-            fake_acquisition
-        ], axis=0)
-
-        if not Spots2['cell_label'].isna().all() :
-            fake_cells = reconstruct_cell_data(
+        try :
+            Spots2 = load_spots(spots2_key)
+            fake_acquisition = reconstruct_acquisition_data(
                 Spots=Spots2,
                 max_id=max_id,
+                voxel_size = voxel_size,
+                filename= os.path.basename(spots2_key),
             )
-
-            cell_result_dataframe = pd.concat([
-                cell_result_dataframe,
-                fake_cells
+            result_dataframe = pd.concat([
+                result_dataframe,
+                fake_acquisition
             ], axis=0)
 
-        max_id +=1
-        acquisition_id2 = fake_acquisition.iloc[0].at['acquisition_id']
+            if not Spots2['cell_label'].isna().all() :
+                fake_cells = reconstruct_cell_data(
+                    Spots=Spots2,
+                    max_id=max_id,
+                    filename= os.path.basename(spots2_key)
+                )
+
+                cell_result_dataframe = pd.concat([
+                    cell_result_dataframe,
+                    fake_cells
+                ], axis=0)
+
+            max_id +=1
+            acquisition_id2 = fake_acquisition.iloc[0].at['acquisition_id']
+        except ValueError as e :
+            sg.popup("Could not reconstruct coordinates from selected file (Spots 2)")
+            traceback.print_exception(e)
+            return global_coloc_df, cell_coloc_df, max_id
 
     else :
         acquisition_id2 = spots2_key

small_fish_gui/pipeline/spots.py

@@ -50,8 +50,7 @@ def compute_Spots(
     if type(cluster_id) == type(None) : #When user doesn't select cluster
         cluster_id = [np.nan]*len(spots)
 
-    index = list(zip(*spots))
-    index = tuple(index)
+    index = tuple(spots.T.tolist())
     spot_intensities_list = list(image[index])
     if type(nucleus_label) != type(None) :
         if nucleus_label.ndim == 2 :
@@ -116,33 +115,26 @@ def reconstruct_acquisition_data(
         ) -> pd.DataFrame:
     """
     Aim : creating a acquisition to add to result_dataframe from loaded spots for co-localization use  
-
-    **Needed keys for colocalization**
-        * acquisition_id
-        * name
-        * spots : np.ndarray[int] (nb_spots, nb_coordinates)
-        * clusters : np.ndarray[int] (nb_cluster, nb_coordinate + 2)
-        * spots_cluster_id : list[int]
-        * voxel_size : tuple[int]
-        * shape : tuple[int]
-        * filename : str
     """
-    
+    max_id = int(max_id)
     spots = reconstruct_spots(Spots['coordinates'])
     has_clusters = not Spots['cluster_id'].isna().all()
     spot_number = len(spots)
 
     if has_clusters :
 
-        clusters = np.empty(shape=(0,5), dtype=int) #useless for coloc only needded in columns to enable coloc on clusters
-        spot_cluster_id = Spots['cluster_id'].to_numpy().astype(int).tolist()
+        clusters = np.empty(shape=(0,5), dtype=int)
+        spot_cluster_id = Spots['cluster_id'].to_numpy().astype(int)
+        clustered_spots = spots[spot_cluster_id != -1]
+        print("clustered_spots : ", clustered_spots)
 
         new_acquisition = pd.DataFrame({
             'acquisition_id' : [max_id + 1],
-            'name' : ["loaded_spots_{}".format(max_id + 1)],
+            'name' : ["(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])],
             'threshold' : [0],
             'spots' : [spots],
-            'clusters' : [clusters],
+            'clusters' : [clusters.tolist()],
+            'clustered_spots_coords' : [clustered_spots.tolist()],
             'spots_cluster_id' : [spot_cluster_id],
             'spot_number' : [spot_number],
             'filename' : [filename],
@@ -151,7 +143,7 @@ def reconstruct_acquisition_data(
     else :
         new_acquisition = pd.DataFrame({
             'acquisition_id' : [max_id + 1],
-            'name' : ["loaded_spots_{}".format(max_id + 1)],
+            'name' : ["(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])],
             'threshold' : [0],
             'spots' : [spots],
             'spot_number' : [spot_number],
@@ -159,6 +151,11 @@ def reconstruct_acquisition_data(
             'voxel_size' : [voxel_size],
         })
 
+    print("Reconstructed acquisition : \n", new_acquisition)
+    print("\n", new_acquisition.columns)
+    if 'clusters' in new_acquisition.columns :
+        print("\n", new_acquisition['clusters'])
+
     return new_acquisition
 
 def reconstruct_spots(
@@ -175,6 +172,7 @@ def reconstruct_spots(
 def reconstruct_cell_data(
         Spots : pd.DataFrame,
         max_id : int,
+        filename : str,
         ) :
     
     has_cluster = not Spots['cluster_id'].isna().all()
@@ -199,7 +197,7 @@ def reconstruct_cell_data(
         cell['clustered_spot_number'] = cell['clustered_spots_coords'].apply(len)
 
     cell['acquisition_id'] = max_id + 1
-    cell['name'] = "loaded_spots_{}".format(max_id + 1)
+    cell['name'] = "(loaded_spots)_{}".format(filename.split('.', maxsplit=1)[0])
     cell = cell.rename(columns={"cell_label": "cell_id"})
 
     return cell

{small_fish_gui-2.1.1.dist-info → small_fish_gui-2.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 2.1.1
+Version: 2.1.3
 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/SmallFishGUI/small_fish_gui
 Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
@@ -131,4 +131,8 @@ You are all set! Try it yourself or check the [get started](https://github.com/2
 
 ## Developement
 Bugs to fix :
-* Use of load button during co-localization quantification yields wrongs results  
+* Use of load button during co-localization quantification yields diffrent results than when testing from memory :
+    --> Shown results are correct and consistent with results from memory
+    --> But background (i.e cell_id = 0) is treated as a cell instead of being filtered
+    --> But cells on edges are NOT removed from quantification (they are if test is performed from memory)
+    --> But Cluster related metrics are not computed when test is performed from save

{small_fish_gui-2.1.1.dist-info → small_fish_gui-2.1.3.dist-info}/RECORD

@@ -1,8 +1,7 @@
-small_fish_gui/__init__.py,sha256=CeLyp2zV0AfjMKoP3uqVfIT1j05NhBfc90HKwtFJhCU,2163
+small_fish_gui/__init__.py,sha256=LXbX5bfmwGeIZqpQAvwXrknqBfev-XlPYsJqXKB2Ch8,2163
 small_fish_gui/__main__.py,sha256=xwpFMDuo0kkYvPamyhlTHJ68bymDfbRpPzKy3SKwezY,1639
 small_fish_gui/hints.py,sha256=NEKqCbjXF3guHnc1dzq_LYYGlTxIV6z6wtdwVlmgHos,3349
 small_fish_gui/main_menu.py,sha256=z0ZlidWNGHLYYnBx2Z1i2IX_EGQr-HtIlsOQl-yTw4o,6273
-small_fish_gui/small_fish_gui.code-workspace,sha256=GbzU4Vx0xJV2o86UOa-FA83na5mGxSD6Efeb1QFBMlM,60
 small_fish_gui/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
 small_fish_gui/batch/__init__.py,sha256=ku2_Yate-UG89Q0BmE2B9kFV4kOz-u9Lf2lj6VsdFXs,127
 small_fish_gui/batch/input.py,sha256=mqnP8LBhyNbtlcqjVlUiVeuHw4YxOX3GgzJbq03isKE,1477
@@ -13,12 +12,11 @@ small_fish_gui/batch/prompt.py,sha256=_WZB-O3oYp8rRdEuf3r8o-ML0EWQn6UTuJVaW2OgpT
 small_fish_gui/batch/test.py,sha256=FcoCngSeueociwVoG8V3C6lQO7rrRHUfIVA2hJKr4v4,213
 small_fish_gui/batch/update.py,sha256=Gv1805-xUtrJ3BK0HdflBSnSFAEB5RmnAPk6peAR9CA,6169
 small_fish_gui/batch/utils.py,sha256=apHxp72OdjTSUyj4ZwN75NYc12Am4m7N9Sw03TrjLMk,1870
-small_fish_gui/batch/values.txt,sha256=9QpmRfZ5AuDByZFzkHxTESKV6bnZMH5DtPIGbMmLsXY,999
 small_fish_gui/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_BM,920
 small_fish_gui/gui/_napari_widgets.py,sha256=9gfikNMLZmeWY9tosD19aGmw4Ulf-BMo8erehJ4KU1k,35321
 small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
-small_fish_gui/gui/layout.py,sha256=CkQNmAWkpaz7WsdG-dp-IOaIxAFrJWLmA7cty3BkQzc,30878
-small_fish_gui/gui/napari_visualiser.py,sha256=5Dk9wJbnmxgNZ3upiQtOrtAr2CT700qkvNQvGsHHdsw,14834
+small_fish_gui/gui/layout.py,sha256=72RZI4Vt5WwZH9cx8SfOCWsZox0udG3Ck3YE_c-aiQ4,30927
+small_fish_gui/gui/napari_visualiser.py,sha256=eU2kqp16EHA3NwbGFBZAiTOiAI_K4zbnMOCtbW4fNuM,14978
 small_fish_gui/gui/prompts.py,sha256=vWLLJZ7jdYIbjT71qHGiE1o9-pTrc607shnKW6EZi8I,18361
 small_fish_gui/gui/testing.ipynb,sha256=2E51kT3BcXvOvOSdmYIy4Cxbe-4HtnOjzPTZQHDZJJw,69148
 small_fish_gui/gui/theme.py,sha256=30nujS48ZRdD1HVbzdEBkiAWlhow1AGgXSQNZcGEsaQ,118
@@ -27,22 +25,22 @@ small_fish_gui/interface/__init__.py,sha256=nqMwHG-l1yMm8iaD6hhCdji5RiKImzNFQcbd
 small_fish_gui/interface/default_settings.py,sha256=vI4-Pl_MpAGuCp7SjWdnpYvWwde_3rfvm9Mb_smaDho,3442
 small_fish_gui/interface/image.py,sha256=0icuHuKFuSZ-YUTIskz-S2HcJ3wXtOrW37iPg8tknHg,3440
 small_fish_gui/interface/inoutput.py,sha256=toB2SNNZNiupZTT2-zQKJ6ewI-_DJTVrXIkdq8TMWXY,5793
-small_fish_gui/interface/settings.json,sha256=8-PCnEJLsoFdkhAeJvKtOiuhBjTcA7CXqnG_IsZAqhI,1402
+small_fish_gui/interface/settings.json,sha256=WqMjgN1Ex01hXruJ1Kkho4nPi9PbEPpOIplT5IIkHxQ,1366
+small_fish_gui/interface/testing.ipynb,sha256=I8iGdcYsds4iBxL417D_PXt7bZcEkHAjWAgXA9DNlSM,323719
 small_fish_gui/interface/testing.py,sha256=AUdqmFJ6kBvFTOLRfZZJBBe3nm1key2bGpUDXJRaueI,2561
 small_fish_gui/interface/user_settings.py,sha256=vMpj-s9tzMKQy1CdJ3SO-6yAknU-ZIMT0RZQs8WAGPY,2620
 small_fish_gui/pipeline/__init__.py,sha256=Oww6dcuvnktl5jFKLriz8ZXObKo9MkneE739A8C1reY,739
 small_fish_gui/pipeline/_bigfish_wrapers.py,sha256=WcIu5HLc4bUuU8qmsINP5snXef3Tx9zJDNKES-SiftA,9776
-small_fish_gui/pipeline/_colocalisation.py,sha256=m6wRgf_nESqvkvkD2RRyTj3ekKKvk43ehvXZ-sXYX84,21714
+small_fish_gui/pipeline/_colocalisation.py,sha256=r96rrWS5lim5bPCcoQMs83DRApCGxJ3ADruFhhYHxN0,22228
 small_fish_gui/pipeline/_custom_errors.py,sha256=tQ-AUhgzIFpK30AZiQQrtHCHyGVRDdAoIjzL0Fk-1pA,43
 small_fish_gui/pipeline/_preprocess.py,sha256=zfwhNoAUkVv1TYlyffNQkSTitMXTDokADabBeHuB58U,15766
-small_fish_gui/pipeline/actions.py,sha256=lPKyX12qEJNnQ4ArYqCRkLrFzwzGgIEl1_HpSFtTMKo,20476
+small_fish_gui/pipeline/actions.py,sha256=dtRCf_UKg-Y9uV1jCBeASeuR7-pZ8dHVEYHs7MW-0pg,21263
 small_fish_gui/pipeline/detection.py,sha256=IE0Wf9NaHcxkCv1cjrOdyfnQUzv8SlXilIT7KI8INP4,35988
 small_fish_gui/pipeline/segmentation.py,sha256=m9XW8XiWCSpGFdi6It6RkeDYTiKtNhfj30kUSBG8pNo,32023
-small_fish_gui/pipeline/spots.py,sha256=3kMe404RHOsNLRZQV6RdpxrHqaRRiGK4_qKSx6jesDM,6738
+small_fish_gui/pipeline/spots.py,sha256=lG9hvn0MqnDWUr2VfSEm8LHoprSlGoDHQFuQGlJHaxM,6807
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
-small_fish_gui/pipeline/testing.ipynb,sha256=zIjnWwsqCBUqydvFx3n4R3_SlrBSwgWjDt50zn4SNgI,339174
 small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
-small_fish_gui-2.1.1.dist-info/METADATA,sha256=796rUUMhbnBHdlSsaXT0lkq4aO14MR5j4iQWxyX8064,6166
-small_fish_gui-2.1.1.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-small_fish_gui-2.1.1.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-2.1.1.dist-info/RECORD,,
+small_fish_gui-2.1.3.dist-info/METADATA,sha256=pFbXtb_Zd3RskgJg-chYrG11YZL32xahnim4TpuTusk,6553
+small_fish_gui-2.1.3.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+small_fish_gui-2.1.3.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-2.1.3.dist-info/RECORD,,

small_fish_gui/batch/values.txt

@@ -1,65 +0,0 @@
-List of keys for batch 'values' dict instance :
-
-Batch_folder 
-0
-image_path 
-3D stack 
-multichannel 
-Dense regions deconvolution 
-do_cluster_computation 
-Segmentation 
-Napari correction 
-x 
-y 
-z 
-c 
-t 
-cyto_model_name 
-cytoplasm_channel 
-cytoplasm_diameter 
-nucleus_model_name 
-nucleus channel 
-nucleus_diameter 
-segment_only_nuclei 
-show_segmentation 
-saving path 
-filename 
-threshold 
-threshold penalty 
-channel to compute 
-voxel_size_z 
-voxel_size_y 
-voxel_size_x 
-spot_size_z 
-spot_size_y 
-spot_size_x 
-log_kernel_size_z 
-log_kernel_size_y 
-log_kernel_size_x 
-minimum_distance_z 
-minimum_distance_y 
-minimum_distance_x 
-nucleus channel signal 
-alpha 
-beta 
-gamma 
-deconvolution_kernel_z 
-deconvolution_kernel_y 
-deconvolution_kernel_x 
-cluster size 
-min number of spots 
-show_interactive_threshold_selector 
-spots_extraction_folder 
-spots_filename 
-do_spots_csv 
-do_spots_excel 
-do_spots_feather 
-output_folder 
-batch_name 
-save segmentation 
-save detection 
-extract spots 
-csv 
-xlsx 
-feather 
-2