small-fish-gui 1.9.0__py3-none-any.whl → 1.9.2__py3-none-any.whl

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__ = "1.9.0"
+__version__ = "1.9.2"

small_fish_gui/batch/pipeline.py

@@ -120,7 +120,7 @@ def batch_pipeline(
         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 = launch_detection(
+            parameters, frame_result, spots, clusters, spot_cluster_id = launch_detection(
                 image,
                 other_image,
                 parameters,
@@ -139,7 +139,7 @@ def batch_pipeline(
         if parameters['save detection'] :
             if parameters['do_cluster_computation'] : 
                 if len(clusters) > 0 :
-                    spots_list = [spots, clusters[:,:parameters['dim']]]
+                    spots_list = [spots, clusters[:,:-2]]
                 else : spots_list = [spots]
             else : spots_list = [spots]
             output_spot_tiffvisual(
@@ -166,6 +166,7 @@ def batch_pipeline(
                     user_parameters=parameters,
                     image=image,
                     spots=spots,
+                    cluster_id=spot_cluster_id,
                     nucleus_label= nucleus_label,
                     cell_label= cytoplasm_label,
                 )
@@ -178,6 +179,7 @@ def batch_pipeline(
         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,

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     Outdated.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=(0,3), 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_clusters = np.empty(shape=(0,5), dtype=int)
             new_cluster_id = -1 * np.ones(len(new_spots))
             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/pipeline/detection.py

@@ -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
 
@@ -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,

{small_fish_gui-1.9.0.dist-info → small_fish_gui-1.9.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 1.9.0
+Version: 1.9.2
 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

{small_fish_gui-1.9.0.dist-info → small_fish_gui-1.9.2.dist-info}/RECORD

@@ -2,7 +2,7 @@ small_fish_gui/.readthedocs.yaml,sha256=r2T0e_In8X8l0_ZwgPvuoWQ9c0PE9bSpFzV2W6Ez
 small_fish_gui/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
 small_fish_gui/README.md,sha256=4RpEXKZW5vH6sUWeZb88yr1TLLPi20PqOk7KdA9O9Hk,4234
 small_fish_gui/Segmentation example.jpg,sha256=opfiSbjmfF6z8kBs08sg_FNR2Om0AcMPU5sSwSLHdoQ,215038
-small_fish_gui/__init__.py,sha256=NAO9zD3llJ5ST2ZjY5DmlJ5Yncl50TO84Gp5568YQQ8,1941
+small_fish_gui/__init__.py,sha256=CweT7xLrnaM2nluNztpNf3JaNncL7gHLFz2SvVG1iZs,1941
 small_fish_gui/__main__.py,sha256=jjFNnf-l4jCJI16epq2KOaKmgtUAe9lSNdPj5fpxrDk,1143
 small_fish_gui/hints.py,sha256=_AhC-Th36ELxinjMyGtjIqJfZkISPr1YwhQ9ifD9Kj4,1926
 small_fish_gui/napari_detection_example.png,sha256=l5EZlrbXemLiGqb5inSVsD6Kko1Opz528-go-fBfrw8,977350
@@ -12,7 +12,7 @@ small_fish_gui/.github/workflows/python-publish.yml,sha256=5Ltnuhw9TevhzndlBmdUg
 small_fish_gui/batch/__init__.py,sha256=ku2_Yate-UG89Q0BmE2B9kFV4kOz-u9Lf2lj6VsdFXs,127
 small_fish_gui/batch/input.py,sha256=mqnP8LBhyNbtlcqjVlUiVeuHw4YxOX3GgzJbq03isKE,1477
 small_fish_gui/batch/integrity.py,sha256=jIJH0c_M_7gSET32iKWEznHIad0OwPNvJurA9rivTJ0,4851
-small_fish_gui/batch/pipeline.py,sha256=ZFb1cGinm-4WLy1vpvPBFA_MvUXQ4UvXkYA74en670c,9065
+small_fish_gui/batch/pipeline.py,sha256=EUUY0L6JvUYyF1SqJ1KdQHKKR1jhxsHSCyBm7nnB7mU,9157
 small_fish_gui/batch/prompt.py,sha256=Ob6Cml3IJTInMJ_9kSwLOKzwna7igbk91D2eaA7I1bo,18849
 small_fish_gui/batch/test.py,sha256=q04a1YstnDsxy2Bi5563BfcOU-O3VPE9c5WSJjvFjMg,211
 small_fish_gui/batch/update.py,sha256=AFG2oW5zfbNPJbb1jqbkMexPB8NoR4ZoftqpO3cAsok,5042
@@ -23,7 +23,7 @@ small_fish_gui/gui/_napari_widgets.py,sha256=8IMppaPZU37ANdZwTZOhwqCEly0hokzYL7U
 small_fish_gui/gui/animation.py,sha256=rnNP5FPp06Hu-R33c4AVTCknALBbxT2YlsKFCXHAp9k,981
 small_fish_gui/gui/help_module.py,sha256=XvGCNIcEGRG8ESJ55poCPhBM60Bl4w_ZxoVp-Ev6lTo,9612
 small_fish_gui/gui/layout.py,sha256=cA8ddzwbxVqTl5-VOoKvYKP0Fki17x2dczidSdW3ayA,14186
-small_fish_gui/gui/napari_visualiser.py,sha256=IZEOTAlCoj-w9M9ubm3VTiEJH-Li5zm9mJFkPK-kmJ4,14733
+small_fish_gui/gui/napari_visualiser.py,sha256=BSoLZtBBdbL407xrio3ZzaU_ZdP7I2T34-zQFntxwEs,14539
 small_fish_gui/gui/prompts.py,sha256=akphsDghaUngmqz3yBpyMPeTrRfye-Flkyixc9JSs74,15406
 small_fish_gui/gui/testing.ipynb,sha256=5xoMDR2a3aa4q8KoEoJ22HrcWDyHkCF4arVeVVm7ovs,71500
 small_fish_gui/gui/screenshot/general_help_screenshot.png,sha256=X4E6Td5f04K-pBUPDaBJRAE3D5b8fuEdiAUKhkIDr-0,54210
@@ -39,14 +39,14 @@ small_fish_gui/pipeline/_custom_errors.py,sha256=tQ-AUhgzIFpK30AZiQQrtHCHyGVRDdA
 small_fish_gui/pipeline/_preprocess.py,sha256=IrkQp_YCVFPrwElCEn-alpVChfLbR_0KAdb0WV2BfKI,15089
 small_fish_gui/pipeline/_signaltonoise.py,sha256=7A9t7xu7zghI6cr201Ldm-LjJ5NOuP56VSeJ8KIzcUo,8497
 small_fish_gui/pipeline/actions.py,sha256=7DmChUin3Zct7utVKj4zRpSMu4i5m2ctheOevbNCxa8,15745
-small_fish_gui/pipeline/detection.py,sha256=IXSbRRUDzJA8-cX30J-2wHRER2pfEXEF-9TxKCEYF8Q,34527
+small_fish_gui/pipeline/detection.py,sha256=X2SmfHTnb2322PimxkXJ9gEco2cCZQ3eCKhfCRzk6hg,34953
 small_fish_gui/pipeline/main.py,sha256=2Oi6wz9jG9LA2gclTkIeFolJ4AON5AN6fFldOQsaXGw,4829
 small_fish_gui/pipeline/segmentation.py,sha256=MtGOcGWJPaJo7oa0YG2qB7LwDLIogJHCioSQxFecUqc,19911
 small_fish_gui/pipeline/spots.py,sha256=9hNOGnOZhrtrIORt8UGBcI-SGCh1XftcUGerkBwN-QY,2201
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/testing.ipynb,sha256=eMynROxPIa5uW6E2nb_CwA4X4Peiqa4QS68JcADrAnM,76479
 small_fish_gui/pipeline/utils.py,sha256=run6qtqCAe_mFnE3o1CnmF1xBBmK3ydgc8-jOV9P-_w,448
-small_fish_gui-1.9.0.dist-info/METADATA,sha256=EN_U5bakmWkSKdm2197zNPXWMuFnxS87oLNWSC7vOpM,2567
-small_fish_gui-1.9.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-small_fish_gui-1.9.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-1.9.0.dist-info/RECORD,,
+small_fish_gui-1.9.2.dist-info/METADATA,sha256=Bq71I80yaGJukLnxynPExQGh5i8hwxHKMfi2sreR0YQ,2567
+small_fish_gui-1.9.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+small_fish_gui-1.9.2.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-1.9.2.dist-info/RECORD,,