small-fish-gui 1.8.0__py3-none-any.whl → 1.8.1__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__ = "1.8.0"
+__version__ = "1.8.1"

small_fish_gui/batch/pipeline.py

@@ -137,7 +137,10 @@ def batch_pipeline(
                 raise(error)
         
         if parameters['save detection'] :
-            if parameters['do_cluster_computation'] : spots_list = [spots, clusters[:,:parameters['dim']]]
+            if parameters['do_cluster_computation'] : 
+                if len(clusters) > 0 :
+                    spots_list = [spots, clusters[:,:parameters['dim']]]
+                else : spots_list = [spots]
             else : spots_list = [spots]
             output_spot_tiffvisual(
                 image,

small_fish_gui/batch/prompt.py

@@ -45,18 +45,18 @@ def batch_promp(
     #Input tab
     input_layout = _input_parameters_layout(
         ask_for_segmentation=True,
-        is_3D_stack_preset= preset.setdefault("3D stack" ,False),
+        is_3D_stack_preset= preset.setdefault("is_3D_stack" ,False),
         time_stack_preset=False,
-        multichannel_preset=preset.setdefault("multichannel" ,False),
-        do_dense_regions_deconvolution_preset=preset.setdefault("Dense regions deconvolution" ,False),
+        multichannel_preset=preset.setdefault("is_multichannel" ,False),
+        do_dense_regions_deconvolution_preset=preset.setdefault("do_dense_regions_deconvolution" ,False),
         do_clustering_preset= preset.setdefault("do_cluster_computation", False),
         do_Napari_correction=False,
-        do_segmentation_preset= preset.setdefault("Segmentation", False),
+        do_segmentation_preset= preset.setdefault("segmentation_done", False),
     )
     input_layout += [[sg.Button('Ok')]]
     input_tab = sg.Tab("Input", input_layout)
 
-    napari_correction_elmt = get_elmt_from_key(input_tab, key='Napari correction')
+    napari_correction_elmt = get_elmt_from_key(input_tab, key='show_napari_corrector')
 
     #Maptab
     map_layout = _ask_channel_map_layout(
@@ -86,7 +86,7 @@ def batch_promp(
     
     apply_segmentation_button = sg.Button('apply', key='apply-segmentation')
     segmentation_layout += [[apply_segmentation_button]]
-    seg_keys_to_hide = ['show segmentation', 'saving path', 'filename']
+    seg_keys_to_hide = ['show segmentation', 'saving path', 'filename', 'other_nucleus_image']
     segmentation_tab = sg.Tab("Segmentation", segmentation_layout, visible=False)
 
     #Detection tab
@@ -228,10 +228,10 @@ def batch_promp(
                 print("Welcome to small fish batch analysis. Please start by loading some files and setting parameters.")
 
             batch_folder = values.get('Batch_folder')
-            is_multichanel = values.get('multichannel')
-            is_3D = values.get('3D stack')
-            do_segmentation = values.get('Segmentation')
-            do_dense_regions_deconvolution = values.get('Dense regions deconvolution')
+            is_multichanel = values.get('is_multichannel')
+            is_3D = values.get('is_3D_stack')
+            do_segmentation = values.get('do_segmentation')
+            do_dense_regions_deconvolution = values.get('do_dense_regions_deconvolution')
             do_clustering = values.get('do_cluster_computation')
 
             if type(batch_folder) != type(None)  and event == 'Load':

small_fish_gui/gui/layout.py

@@ -227,18 +227,14 @@ def _input_parameters_layout(
 
 ) :
     layout_image_path = path_layout(['image path'], header= "Image")
-    layout_image_path += bool_layout(['is_3D_stack', 'is_multichannel'], preset= [is_3D_stack_preset, time_stack_preset, multichannel_preset])
+    layout_image_path += bool_layout(['3D stack', 'Multichannel stack'], keys=['is_3D_stack', 'is_multichannel'], preset= [is_3D_stack_preset, multichannel_preset])
     
-    if ask_for_segmentation : 
-        layout_image_path += bool_layout(
-            ['do_dense_regions_deconvolution', 'do_cluster_computation', 'Segmentation', 'show_napari_corrector'], 
-            preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_segmentation_preset, do_Napari_correction], 
-            header= "Pipeline settings")
-    else : 
-        layout_image_path += bool_layout(
-            ['do_dense_regions_deconvolution', 'do_cluster_computation', 'show_napari_corrector'], 
-            preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_Napari_correction], 
-            header= "Pipeline settings")
+    layout_image_path += bool_layout(
+        ['Dense regions deconvolution', 'Compute clusters', 'Cell segmentation', 'Open Napari corrector'],
+        keys= ['do_dense_regions_deconvolution', 'do_cluster_computation', 'do_segmentation', 'show_napari_corrector'], 
+        preset= [do_dense_regions_deconvolution_preset, do_clustering_preset, do_segmentation_preset, do_Napari_correction], 
+        header= "Pipeline settings")
+
 
     return layout_image_path
 

small_fish_gui/hints.py

@@ -8,7 +8,6 @@ class pipeline_parameters(TypedDict) :
             """
             At run time is a regular dict instance, this class is used for keys hinting
             """
-            is_3D_stack : bool
             alpha : float
             beta : float
             channel_to_compute : int
@@ -31,6 +30,7 @@ class pipeline_parameters(TypedDict) :
             minimum_distance_x : float
             minimum_distance_y : float
             minimum_distance_z : float
+            is_3D_stack : bool
             is_multichannel : bool
             show_napari_corrector : bool
             nucleus_channel_signal : int

{small_fish_gui-1.8.0.dist-info → small_fish_gui-1.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: small_fish_gui
-Version: 1.8.0
+Version: 1.8.1
 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-1.8.0.dist-info → small_fish_gui-1.8.1.dist-info}/RECORD

@@ -2,9 +2,9 @@ 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=AOkS4cxFmXcSkoisvufIeqzeETWYnRPA-bAQwDeuwps,1941
+small_fish_gui/__init__.py,sha256=biAaT2rtp7S5QW4_IUAfG4ey2uKsf3c8m7gqNFezrj4,1941
 small_fish_gui/__main__.py,sha256=jjFNnf-l4jCJI16epq2KOaKmgtUAe9lSNdPj5fpxrDk,1143
-small_fish_gui/hints.py,sha256=nSnaz-vs2CeOqRj8MqxnIxYCf8fhwNYUigJTImm1nM8,1926
+small_fish_gui/hints.py,sha256=_AhC-Th36ELxinjMyGtjIqJfZkISPr1YwhQ9ifD9Kj4,1926
 small_fish_gui/napari_detection_example.png,sha256=l5EZlrbXemLiGqb5inSVsD6Kko1Opz528-go-fBfrw8,977350
 small_fish_gui/requirements.txt,sha256=9OMfUAnLdHevq6w_fVoDmVmkSMJeFofkOK_86_fu9C0,321
 small_fish_gui/utils.py,sha256=LM6QW2ono_LIRv7JXIIq7ZxxbDXqBtZ5uR9gjKJfwM8,1903
@@ -12,8 +12,8 @@ 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=ka43HQpScvxZ1HY1kSPUUCu0igbevT0BD8dWyY5ZlNA,8961
-small_fish_gui/batch/prompt.py,sha256=S_SX30SPVda4WjqffF1Pnnzkk84o9uIO-BduA5Iv8NQ,18796
+small_fish_gui/batch/pipeline.py,sha256=ZFb1cGinm-4WLy1vpvPBFA_MvUXQ4UvXkYA74en670c,9065
+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
 small_fish_gui/batch/utils.py,sha256=JGRgaPcNQ5V2Hr8ObtmmMKqm3fB237Iym6aBawWY8Oo,1782
@@ -22,7 +22,7 @@ small_fish_gui/gui/__init__.py,sha256=xQ_BfYcnQmKZtx_0leO4OmbkLNLv49ZPqEu_UXMgmD
 small_fish_gui/gui/_napari_widgets.py,sha256=8IMppaPZU37ANdZwTZOhwqCEly0hokzYL7UIVIixGns,3022
 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=fy1Ev952dJpVHk5BV0E8rjjUSqdaiEb3TDTb5smlQu8,14395
+small_fish_gui/gui/layout.py,sha256=cA8ddzwbxVqTl5-VOoKvYKP0Fki17x2dczidSdW3ayA,14186
 small_fish_gui/gui/napari.py,sha256=XiahTyq7QEQAuF6EK3-e--3-A8yBPVn0oaVZZyJo0qo,8607
 small_fish_gui/gui/prompts.py,sha256=1CVXatzS4edDI0bLSSBKaEEJSWaNQPtL__1AzbPYLdQ,15391
 small_fish_gui/gui/screenshot/general_help_screenshot.png,sha256=X4E6Td5f04K-pBUPDaBJRAE3D5b8fuEdiAUKhkIDr-0,54210
@@ -44,7 +44,7 @@ small_fish_gui/pipeline/segmentation.py,sha256=dmQ9afugX7wMVSVwpJ15EZ-KEH7fbeddV
 small_fish_gui/pipeline/spots.py,sha256=mam9w9qi8MGmMirOcWFGIaz4nsxntPyZhetV7uSga80,1965
 small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
 small_fish_gui/pipeline/utils.py,sha256=run6qtqCAe_mFnE3o1CnmF1xBBmK3ydgc8-jOV9P-_w,448
-small_fish_gui-1.8.0.dist-info/METADATA,sha256=kcahOCZBF7dBSPirS4RAfctLYprcVTXrOM5W7A8O5Tg,2545
-small_fish_gui-1.8.0.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
-small_fish_gui-1.8.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
-small_fish_gui-1.8.0.dist-info/RECORD,,
+small_fish_gui-1.8.1.dist-info/METADATA,sha256=SwVT6szwgOjdHth8Czp1G-PkeC7xELGZJZWG0jUmAgA,2545
+small_fish_gui-1.8.1.dist-info/WHEEL,sha256=C2FUgwZgiLbznR-k0b_5k3Ai_1aASOXDss3lzCUsUug,87
+small_fish_gui-1.8.1.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-1.8.1.dist-info/RECORD,,