small-fish-gui 2.0.3__tar.gz → 2.1.1__tar.gz

{small_fish_gui-2.0.3 → small_fish_gui-2.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: small_fish_gui
-Version: 2.0.3
+Version: 2.1.1
 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/SmallFishGUI/small_fish_gui
 Project-URL: Wiki, https://github.com/SmallFishGUI/small_fish_gui/wiki
@@ -36,7 +36,7 @@ Description-Content-Type: text/markdown
 # Small Fish - A User-Friendly Graphical Interface for smFISH Image Quantification
 
 [![License: BSD-2-Clause](https://img.shields.io/badge/License-BSD_2--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
- [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+ [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 
 **Small Fish** is a python application for smFish image analysis. It provides a ready to use graphical interface to synthetize state-of-the-art scientific packages into an automated workflow. Small Fish is designed to simplify images quantification and analysis for people without coding skills. 
 
@@ -83,22 +83,27 @@ Analysis can be performed either fully interactively throught a Napari interface
 
 ### General setup
 
-If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/).
+If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/); but any distribution should work.
 
-It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
+It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.9/library/venv.html) environnement to install small fish.
 
+As of version 2.1.0 Small Fish runs on python 3.12.
+
+If you are using **conda** or **miniconda**
 ```bash
-conda create -n small_fish python=3.9
+conda create -n small_fish python=3.12
 conda activate small_fish
 ```
-Then download the small_fish package : 
+
+If you are using **venv**, after installing the official python 3.12, python-venv **and** *python-tk* .
 ```bash
-pip install small_fish_gui
+python3.12 -m venv python_env/small_fish
+source python_env/small_fish/bin/activate
 ```
-Results visualisation is achieved through *Napari* which you can install with :
 
+Then download and install the small_fish package with : 
 ```bash
-pip install napari[all]
+pip install small_fish_gui
 ```
 
 ### Setting up GPU
@@ -123,3 +128,7 @@ python -m small_fish_gui
 ```
 
 You are all set! Try it yourself or check the [get started](https://github.com/2Echoes/small_fish_gui/wiki/Get-started) section in the wiki.
+
+## Developement
+Bugs to fix :
+* Use of load button during co-localization quantification yields wrongs results  

{small_fish_gui-2.0.3 → small_fish_gui-2.1.1}/README.md

@@ -1,7 +1,7 @@
 # Small Fish - A User-Friendly Graphical Interface for smFISH Image Quantification
 
 [![License: BSD-2-Clause](https://img.shields.io/badge/License-BSD_2--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
- [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.9+](https://img.shields.io/badge/python-3.9+-blue.svg)](https://www.python.org/downloads/)
+ [![GitHub stars](https://img.shields.io/github/stars/SmallFishGUI/small_fish_gui.svg?style=social)](https://github.com/SmallFishGUI/small_fish_gui) [![Python 3.12+](https://img.shields.io/badge/python-3.12+-blue.svg)](https://www.python.org/downloads/)
 
 **Small Fish** is a python application for smFish image analysis. It provides a ready to use graphical interface to synthetize state-of-the-art scientific packages into an automated workflow. Small Fish is designed to simplify images quantification and analysis for people without coding skills. 
 
@@ -48,22 +48,27 @@ Analysis can be performed either fully interactively throught a Napari interface
 
 ### General setup
 
-If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/).
+If you don't have a python installation yet I would recommend the [miniconda distribution](https://docs.anaconda.com/free/miniconda/miniconda-other-installer-links/); but any distribution should work.
 
-It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.6/library/venv.html) environnement to install small fish.
+It is higly recommanded to create a specific [conda](https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html) or [virtual](https://docs.python.org/3.9/library/venv.html) environnement to install small fish.
 
+As of version 2.1.0 Small Fish runs on python 3.12.
+
+If you are using **conda** or **miniconda**
 ```bash
-conda create -n small_fish python=3.9
+conda create -n small_fish python=3.12
 conda activate small_fish
 ```
-Then download the small_fish package : 
+
+If you are using **venv**, after installing the official python 3.12, python-venv **and** *python-tk* .
 ```bash
-pip install small_fish_gui
+python3.12 -m venv python_env/small_fish
+source python_env/small_fish/bin/activate
 ```
-Results visualisation is achieved through *Napari* which you can install with :
 
+Then download and install the small_fish package with : 
 ```bash
-pip install napari[all]
+pip install small_fish_gui
 ```
 
 ### Setting up GPU
@@ -88,3 +93,7 @@ python -m small_fish_gui
 ```
 
 You are all set! Try it yourself or check the [get started](https://github.com/2Echoes/small_fish_gui/wiki/Get-started) section in the wiki.
+
+## Developement
+Bugs to fix :
+* Use of load button during co-localization quantification yields wrongs results  

small_fish_gui-2.1.1/error_log.txt

@@ -0,0 +1,374 @@
+version 2.0.2error : `newbyteorder` was removed from the ndarray class in NumPy 2.0. Use `arr.view(arr.dtype.newbyteorder(order))` instead.traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 47, in launch_segmentation
+    new_parameters = ask_input_parameters(user_parameters, ask_for_segmentation= True) #The image is open and stored inside user_parameters
+                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_preprocess.py", line 385, in ask_input_parameters
+    image_input_values = input_image_prompt(
+                         ^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 96, in input_image_prompt
+    image = open_image(im_path)
+            ^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/interface/image.py", line 15, in open_image
+    else : im = read_image(full_path)
+                ^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/big-fish/bigfish/stack/io.py", line 51, in read_image
+    image = tifffile.imread(path)
+            ^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/python_env/small_fish_3.12/lib/python3.12/site-packages/tifffile/tifffile.py", line 1064, in imread
+    return tif.asarray(
+           ^^^^^^^^^^^^
+  File "/home/floric/python_env/small_fish_3.12/lib/python3.12/site-packages/tifffile/tifffile.py", line 4195, in asarray
+    result = self.filehandle.read_array(
+             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/python_env/small_fish_3.12/lib/python3.12/site-packages/tifffile/tifffile.py", line 13922, in read_array
+    result = result.newbyteorder()
+             ^^^^^^^^^^^^^^^^^^^
+AttributeError: `newbyteorder` was removed from the ndarray class in NumPy 2.0. Use `arr.view(arr.dtype.newbyteorder(order))` instead.
+version 2.0.2error : small_fish_gui.gui.prompts.segmentation_prompt() got multiple values for keyword argument 'image'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 67, in launch_segmentation
+    event, values = segmentation_prompt(
+                    ^^^^^^^^^^^^^^^^^^^^
+TypeError: small_fish_gui.gui.prompts.segmentation_prompt() got multiple values for keyword argument 'image'
+version 2.0.2error : 'anisotropy'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 166, in launch_segmentation
+    if not isinstance(values["anisotropy"], (float,int)) :
+                      ~~~~~~^^^^^^^^^^^^^^
+KeyError: 'anisotropy'
+version 2.0.2error : name 'filename' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 241, in launch_segmentation
+    if type(path) != type(None) and filename != '':
+                                    ^^^^^^^^
+NameError: name 'filename' is not defined
+version 2.0.2error : 'filename'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 242, in launch_segmentation
+    if type(path) != type(None) and user_parameters["filename"] != '':
+                                    ~~~~~~~~~~~~~~~^^^^^^^^^^^^
+KeyError: 'filename'
+version 2.0.2error : name 'cytoplasm_model_name' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 253, in launch_segmentation
+    cytoplasm_model_name= cytoplasm_model_name,
+                          ^^^^^^^^^^^^^^^^^^^^
+NameError: name 'cytoplasm_model_name' is not defined
+version 2.0.2error : 'nucleus_segmentation_3D'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 261, in launch_segmentation
+    nucleus_3D_segmentation=user_parameters["nucleus_segmentation_3D"],
+                            ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^
+KeyError: 'nucleus_segmentation_3D'
+version 2.0.2error : name 'show_segmentation' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 325, in launch_segmentation
+    if show_segmentation :
+       ^^^^^^^^^^^^^^^^^
+NameError: name 'show_segmentation' is not defined. Did you mean: 'plot_segmentation'?
+version 2.0.2error : name 'is_3D_stack' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 89, in launch_segmentation
+    values, relaunch = _check_integrity_segmentation_parameters(values, user_parameters, available_channels=available_channels, available_slices=available_slices)
+                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 368, in _check_integrity_segmentation_parameters
+    if is_3D_stack :
+       ^^^^^^^^^^^
+NameError: name 'is_3D_stack' is not defined
+version 2.0.2error : name 'nucleus_image' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 139, in launch_segmentation
+    nuc_image=image[nucleus_channel] if type(nucleus_image) == type(None) else nucleus_image,
+                                             ^^^^^^^^^^^^^
+NameError: name 'nucleus_image' is not defined. Did you mean: 'nucleus_label'?
+version 2.0.2error : name 'nucleus_image' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 139, in launch_segmentation
+    nuc_image=image[nucleus_channel] if type(nucleus_image) == type(None) else nucleus_image,
+                                             ^^^^^^^^^^^^^
+NameError: name 'nucleus_image' is not defined. Did you mean: 'nucleus_label'?
+version 2.0.2error : name 'nucleus_channel' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 139, in launch_segmentation
+    nuc_image=image[nucleus_channel] if type(user_parameters["other_nucleus_image"]) == type(None) else user_parameters["other_nucleus_image"],
+                    ^^^^^^^^^^^^^^^
+NameError: name 'nucleus_channel' is not defined. Did you mean: 'nucleus_label'?
+version 2.0.2error : 'str' object has no attribute 'ndim'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 117, in launch_segmentation
+    cytoplasm_label, nucleus_label = cell_segmentation(
+                                     ^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 232, in cell_segmentation
+    if nuc.ndim >= 3 and not nucleus_3D_segmentation:
+       ^^^^^^^^
+AttributeError: 'str' object has no attribute 'ndim'
+version 2.0.2error : name 'result' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 45, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 101, in add_detection
+    user_parameters, frame_result, spots, clusters, spots_cluster_id = launch_detection(
+                                                                       ^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/detection.py", line 626, in launch_detection
+    spots, threshold = interactive_detection(
+                       ^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 262, in interactive_detection
+    background_remover = _interactive_background_removal(image, voxel_size, **kwargs)
+                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 344, in _interactive_background_removal
+    background_remover = BackgroundRemover(
+                         ^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/_napari_widgets.py", line 792, in __init__
+    "contrast_limits" : [result.min(), result.max()],
+                         ^^^^^^
+NameError: name 'result' is not defined
+version 2.0.2error : 'Column' object is not iterabletraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 322, in coloc_prompt
+    for row in element_dict[f"options_spots{spot_id}_memory"] :
+TypeError: 'Column' object is not iterable
+version 2.0.2error : name 'do_only_nuc' is not definedtraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 55, in <module>
+    nucleus_label, cytoplasm_label, user_parameters = segment_cells(
+                                                      ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 51, in segment_cells
+    nucleus_label, cytoplasm_label, user_parameters = launch_segmentation(
+                                                      ^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/segmentation.py", line 174, in launch_segmentation
+    if not do_only_nuc :
+          ^^^^^^^^^^^
+NameError: name 'do_only_nuc' is not defined
+version 2.0.2error : 'Column' object is not iterabletraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 322, in coloc_prompt
+    for row in element_dict[f"options_spots{spot_id}_memory"] :
+TypeError: 'Column' object is not iterable
+version 2.0.2error : Text.update() got an unexpected keyword argument 'disabled'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 325, in coloc_prompt
+    for elmnt in row : elmnt.update(disabled= is_memory)
+                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+TypeError: Text.update() got an unexpected keyword argument 'disabled'
+version 2.0.2error : 'NoneType' object has no attribute 'get'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 303, in coloc_prompt
+    layout, element_dict = colocalization_layout(spot_list, **default_values)
+                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/layout.py", line 477, in colocalization_layout
+    sg.Input(size=20, key= f"spots{spot_id}_browse", default_text=default_values.get(f"spots{spot_id}_browse"), disabled=element_dict[f"radio_spots{spot_id}_memory"].get()),
+                                                                                                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/python_env/small_fish_3.12/lib/python3.12/site-packages/FreeSimpleGUI/elements/radio.py", line 248, in get
+    return self.TKIntVar.get() == self.EncodedRadioValue
+           ^^^^^^^^^^^^^^^^^
+AttributeError: 'NoneType' object has no attribute 'get'
+version 2.0.2error : 'NoneType' object has no attribute 'get'traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 303, in coloc_prompt
+    layout, element_dict = colocalization_layout(spot_list, **default_values)
+                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/layout.py", line 478, in colocalization_layout
+    print(element_dict[f"radio_spots{spot_id}_memory"].get())
+          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/python_env/small_fish_3.12/lib/python3.12/site-packages/FreeSimpleGUI/elements/radio.py", line 248, in get
+    return self.TKIntVar.get() == self.EncodedRadioValue
+           ^^^^^^^^^^^^^^^^^
+AttributeError: 'NoneType' object has no attribute 'get'
+version 2.0.2error : dict.setdefault() takes no keyword argumentstraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 80, in <module>
+    global_coloc_df, cell_coloc_df, acquisition_id = compute_colocalisation(
+                                                     ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 300, in compute_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key = initiate_colocalisation(result_dataframe)
+                                                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/_colocalisation.py", line 178, in initiate_colocalisation
+    colocalisation_distance, voxel_size, spots1_key, spots2_key, values = coloc_prompt(
+                                                                          ^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/prompts.py", line 303, in coloc_prompt
+    layout, element_dict = colocalization_layout(spot_list, **default_values)
+                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/layout.py", line 478, in colocalization_layout
+    sg.FileBrowse(key=f"spots{spot_id}_browsebutton", initial_folder=default_values.setdefault(f"spots{spot_id}_browsebutton", default_values["working_directory"], disabled=can_use_memory and not default_values.get(f"radio_spots{spot_id}_load"))),
+                                                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+TypeError: dict.setdefault() takes no keyword arguments
+version 2.1.1error : not enough values to unpack (expected 3, got 2)traceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 45, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 114, in add_detection
+    raise(error)
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 101, in add_detection
+    user_parameters, frame_result, spots, clusters, spots_cluster_id, image = launch_detection(
+                                                                              ^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/detection.py", line 626, in launch_detection
+    spots, image, updated_parameters = interactive_detection(
+                                       ^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 291, in interactive_detection
+    dense_region_deconvolver = _interactive_spot_decomposition(
+                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 350, in _interactive_spot_decomposition
+    dense_regions_deconvolver = DenseRegionDeconvolver(
+                                ^^^^^^^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/_napari_widgets.py", line 817, in __init__
+    self.update_dense_regions()
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/_napari_widgets.py", line 834, in update_dense_regions
+    z,y,x = coordinates.T
+    ^^^^^
+ValueError: not enough values to unpack (expected 3, got 2)
+version 2.1.1error : cannot access local variable 'cell_label_layer' where it is not associated with a valuetraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 45, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 101, in add_detection
+    user_parameters, frame_result, spots, clusters, spots_cluster_id, image = launch_detection(
+                                                                              ^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/detection.py", line 663, in launch_detection
+    spots, clusters, new_cluster_radius, new_min_spot_number, nucleus_label, cell_label = correct_spots(
+                                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 160, in correct_spots
+    new_cell_label = cell_label_layer.data
+                     ^^^^^^^^^^^^^^^^
+UnboundLocalError: cannot access local variable 'cell_label_layer' where it is not associated with a value
+version 2.1.1error : cannot access local variable 'new_nucleus_label' where it is not associated with a valuetraceback :
+Traceback (most recent call last):
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/main_menu.py", line 45, in <module>
+    new_result_df, new_cell_result_df, acquisition_id, user_parameters =  add_detection(
+                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/actions.py", line 101, in add_detection
+    user_parameters, frame_result, spots, clusters, spots_cluster_id, image = launch_detection(
+                                                                              ^^^^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/pipeline/detection.py", line 663, in launch_detection
+    spots, clusters, new_cluster_radius, new_min_spot_number, nucleus_label, cell_label = correct_spots(
+                                                                                          ^^^^^^^^^^^^^^
+  File "/home/floric/my_projects/small_fish_gui/src/small_fish_gui/gui/napari_visualiser.py", line 175, in correct_spots
+    return new_spots, new_clusters,  new_cluster_radius, new_min_spot_number, new_nucleus_label, new_cell_label
+                                                                              ^^^^^^^^^^^^^^^^^
+UnboundLocalError: cannot access local variable 'new_nucleus_label' where it is not associated with a value

{small_fish_gui-2.0.3 → small_fish_gui-2.1.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "hatchling.build"
 
 [project]
 name = "small_fish_gui"
-version = "2.0.3"
+version = "2.1.1"
 authors = [
   { name="Slimani Floric", email="floric.slimani@live.fr" },
 ]

small_fish_gui-2.1.1/small_fish_gui.code-workspace

@@ -0,0 +1,7 @@
+{
+	"folders": [
+		{
+			"path": "."
+		}
+	]
+}

{small_fish_gui-2.0.3 → small_fish_gui-2.1.1}/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__ = "2.0.3"
+__version__ = "2.1.1"
 __wiki__ = "https://github.com/2Echoes/small_fish_gui/wiki"
 
 import os, platform

{small_fish_gui-2.0.3 → small_fish_gui-2.1.1}/src/small_fish_gui/batch/prompt.py

@@ -104,7 +104,7 @@ def batch_promp(
     preset["reordered_shape"] =  None
     preset.setdefault("filename", "")
     #Segmentation tab
-    preset.setdefault("other_nucleus_image", default.working_directory)
+    preset.setdefault("other_nucleus_image", "")
     preset.setdefault("cytoplasm_channel", default.detection_channel)
     preset.setdefault("cytoplasm_segmentation_3D", default.do_3D_segmentation)
     preset.setdefault("nucleus_segmentation_3D", default.do_3D_segmentation)

small_fish_gui-2.1.1/src/small_fish_gui/batch/values.txt

@@ -0,0 +1,65 @@
+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