small-fish-gui 2.1.2__py3-none-any.whl → 2.1.3__py3-none-any.whl

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__ = "2.1.2"
+__version__ = "2.1.3"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os, platform

small_fish_gui/gui/napari_visualiser.py

@@ -309,7 +309,10 @@ def interactive_detection(
     if dense_region_deconvolution : updated_parameters.update(dense_region_deconvolver.get_detection_parameters())
     signal = Viewer.layers['raw signal'].data
 
-    spots = Viewer.layers['single spots'].data.astype(np.int32)
+    if 'decovoluted spots' in Viewer.layers :
+        spots = Viewer.layers['decovoluted spots'].data.astype(np.int32)
+    else :
+        spots = Viewer.layers['single spots'].data.astype(np.int32)
 
     return spots, signal, updated_parameters
 

small_fish_gui/pipeline/_colocalisation.py

@@ -359,6 +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'],
@@ -387,7 +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/spots.py

@@ -115,16 +115,6 @@ 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'])
@@ -133,15 +123,18 @@ def reconstruct_acquisition_data(
 
     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(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],
@@ -158,6 +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(

{small_fish_gui-2.1.2.dist-info → small_fish_gui-2.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 2.1.2
+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

{small_fish_gui-2.1.2.dist-info → small_fish_gui-2.1.3.dist-info}/RECORD

@@ -1,4 +1,4 @@
-small_fish_gui/__init__.py,sha256=Ue6wty6U37_1rZ9SUrxmxA9r9ydjn0uACU-SqWHt6CE,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
@@ -16,7 +16,7 @@ small_fish_gui/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_B
 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=72RZI4Vt5WwZH9cx8SfOCWsZox0udG3Ck3YE_c-aiQ4,30927
-small_fish_gui/gui/napari_visualiser.py,sha256=HsHEp2B7lWKFGLQaGI99u3IPaWzsfG1MHJsx_1t0rf0,14844
+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
@@ -31,16 +31,16 @@ small_fish_gui/interface/testing.py,sha256=AUdqmFJ6kBvFTOLRfZZJBBe3nm1key2bGpUDX
 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=n7ULhlaKH2M2mKPgnn9On0NOdG-mqPCGuOgYgo13vA0,21922
+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=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=rL4BLH0BtPQiinpQHqJ3ooq6_DDS_oa4UBdKQTl_-ok,6841
+small_fish_gui/pipeline/spots.py,sha256=lG9hvn0MqnDWUr2VfSEm8LHoprSlGoDHQFuQGlJHaxM,6807
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
-small_fish_gui-2.1.2.dist-info/METADATA,sha256=g5pFqOzoXqyNLC9Bgk2wWfjWTvjtDaM0HK-2zDKOS6s,6553
-small_fish_gui-2.1.2.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
-small_fish_gui-2.1.2.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-2.1.2.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,,