small-fish-gui 2.0.2__py3-none-any.whl → 2.1.0__py3-none-any.whl

small_fish_gui/pipeline/spots.py

@@ -48,7 +48,7 @@ def compute_Spots(
         return pd.DataFrame()
 
     if type(cluster_id) == type(None) : #When user doesn't select cluster
-        cluster_id = [np.NaN]*len(spots)
+        cluster_id = [np.nan]*len(spots)
 
     index = list(zip(*spots))
     index = tuple(index)
@@ -59,14 +59,14 @@ def compute_Spots(
         else :
             in_nuc_list = list(nucleus_label.astype(bool)[index])
     else :
-        in_nuc_list = np.NaN
+        in_nuc_list = np.nan
     if type(cell_label) != type(None) :
         if cell_label.ndim == 3 :
             cell_label_list = list(cell_label[index])
         else :    
             cell_label_list = list(cell_label[index[-2:]]) #Only plane coordinates
     else :
-        cell_label_list = np.NaN
+        cell_label_list = np.nan
     id_list = np.arange(len(spots))
 
     coord_list = list(zip(*index))

small_fish_gui/pipeline/utils.py

@@ -1,4 +1,5 @@
 import numpy as np
+import platform
 
 from math import ceil
 from itertools import zip_longest
@@ -13,4 +14,7 @@ def from_label_get_centeroidscoords(label: np.ndarray):
         n should be replace with 1,2.. according to the axe you wish to access."""
 
     centroid = regionprops_table(label, properties= ["label","centroid"])
-    return centroid
+    return centroid
+  
+def using_mps():
+    return platform.system() == "Darwin" and torch.backends.mps.is_available()

small_fish_gui/README.md → small_fish_gui-2.1.0.dist-info/METADATA

@@ -1,7 +1,42 @@
+Metadata-Version: 2.4
+Name: small_fish_gui
+Version: 2.1.0
+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
+Project-URL: Issues, https://github.com/SmallFishGUI/small_fish_gui/issues
+Author-email: Slimani Floric <floric.slimani@live.fr>
+License-File: LICENSE
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.12
+Requires-Dist: af-eraser>=0.1.0
+Requires-Dist: aicspylibczi>=3.3.1
+Requires-Dist: big-fish-reloaded==0.6.2
+Requires-Dist: cellpose>=4.0.6
+Requires-Dist: czifile>=2019.7.2
+Requires-Dist: freesimplegui>=5.1.1
+Requires-Dist: imageio>=2.34.0
+Requires-Dist: napari-console>=0.0.9
+Requires-Dist: napari-plugin-engine>=0.2.0
+Requires-Dist: napari-plugin-manager>=0.1.0a2
+Requires-Dist: napari-svg>=0.1.10
+Requires-Dist: napari>=0.4.19.post1
+Requires-Dist: napari[all]
+Requires-Dist: numpy>=1.26
+Requires-Dist: openpyxl>=3.1.2
+Requires-Dist: pandas>=2.1.1
+Requires-Dist: pyarrow>=11.0.0
+Requires-Dist: scikit-image>=0.19.1
+Requires-Dist: scikit-learn>=1.3.2
+Requires-Dist: scipy
+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. 
 
@@ -48,22 +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/3.9/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/3.6/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

small_fish_gui-2.1.0.dist-info/RECORD

@@ -0,0 +1,46 @@
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+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/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
+small_fish_gui/batch/integrity.py,sha256=3m3faYeIM6-l5-6butv0sc56dKTz56GNiID0bps_mL8,5085
+small_fish_gui/batch/output.py,sha256=cKZBsO48HaKfxfa6cwcBKw3YRILBCcdC8rpYd2OTEVs,520
+small_fish_gui/batch/pipeline.py,sha256=oVylDQ3v88Wz1BuGoVBTchPGBkVFKRhMMXclSYkr6kY,14462
+small_fish_gui/batch/prompt.py,sha256=LIjzVijpvZ9YShQ2-FRjit2RoJZhSMyebcKnsx_99vs,22001
+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/gui/__init__.py,sha256=idpRSg2FFawF0ydfc7Y8ep6gQ4_jhroL_jZURlRE_BM,920
+small_fish_gui/gui/_napari_widgets.py,sha256=xXa-da5MYEWCpwlnE7LkURXSjxvAcF2EHj9-jm482Rk,34934
+small_fish_gui/gui/animation.py,sha256=MnYsA1kxQZ72L_H0knxOs41lG0ZZv1re7gSgYNmZY00,983
+small_fish_gui/gui/layout.py,sha256=qQVxOvjd0UNSxa9oZaLMZLHiApieqYUWSONulqYF-kQ,30881
+small_fish_gui/gui/napari_visualiser.py,sha256=mipNwfcUDVZSZjlnZDbVe9E4p_2cBsxFDoQX6vqhsbk,13935
+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
+small_fish_gui/gui/tooltips.py,sha256=av_oVmDTT69_wbSlek1mDmnLhB9JUyuEheqVB6rriqw,1376
+small_fish_gui/interface/__init__.py,sha256=nqMwHG-l1yMm8iaD6hhCdji5RiKImzNFQcbdLSf9RLw,519
+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=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/_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/detection.py,sha256=Gi1H01P8n7EsthY1NsyRR407DwXxvrJB9S91aMBfc0A,35961
+small_fish_gui/pipeline/segmentation.py,sha256=rlDxHrbhokEJngmaGTjWHRp06XXraQWUWWUHA4sROq0,32065
+small_fish_gui/pipeline/spots.py,sha256=3kMe404RHOsNLRZQV6RdpxrHqaRRiGK4_qKSx6jesDM,6738
+small_fish_gui/pipeline/test.py,sha256=w4ZMGDmUDXxVgWTlZ2TKw19W8q5gcE9gLMKe0SWnRrw,2827
+small_fish_gui/pipeline/utils.py,sha256=dYV7WAJ375xM5RdaljjxeKvBC1niQvBl1E55SeIiIYo,563
+small_fish_gui-2.1.0.dist-info/METADATA,sha256=sam8sxyfdn6HYGPPtj-3UQnGwNt2pz_e8ZjGTEfbwes,6052
+small_fish_gui-2.1.0.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+small_fish_gui-2.1.0.dist-info/licenses/LICENSE,sha256=-iFy8VGBYs5VsHglKpk4D-hxqQ2jMJaqmfq_ulIzDks,1303
+small_fish_gui-2.1.0.dist-info/RECORD,,

{small_fish_gui-2.0.2.dist-info → small_fish_gui-2.1.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any

small_fish_gui/.github/workflows/python-publish.yml

@@ -1,39 +0,0 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
-
-# This workflow uses actions that are not certified by GitHub.
-# They are provided by a third-party and are governed by
-# separate terms of service, privacy policy, and support
-# documentation.
-
-name: Upload Python Package
-
-on:
-  release:
-    types: [published]
-
-permissions:
-  contents: read
-
-jobs:
-  deploy:
-
-    runs-on: ubuntu-latest
-
-    steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-    - name: Build package
-      run: python -m build
-    - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}

small_fish_gui/LICENSE

@@ -1,24 +0,0 @@
-BSD 2-Clause License
-
-Copyright (c) 2023, Floric Slimani
-
-Redistribution and use in source and binary forms, with or without
-modification, are permitted provided that the following conditions are met:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
-SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
-CAUSED AND 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.

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

small_fish_gui/default_values.py

@@ -1,51 +0,0 @@
-""""
-Constant submodule to have a common reference for parameters default values
-"""
-import os
-
-#Image
-IS_MULTICHANNEL = False
-IS_3D_STACK = False
-CHANNEL = 0
-NUC_CHANNEL = 1
-
-#Segmentation
-FLOW_THRESHOLD = 0.4
-CELLPROB_THRESHOD = 0.
-CYTO_MODEL = "cpsam"
-NUC_MODEL = "cpsam"
-CYTO_DIAMETER = 90
-NUC_DIAMETER = 60
-ANISOTROPY = 1. 
-SHOW_SEGMENTATION = True
-SEGMENT_ONLY_NUCLEI = False
-DO_3D_SEMGENTATION = False
-VISUAL_PATH = os.getcwd()
-SAVE_SEGMENTATION_VISUAL = False
-
-#Detection
-THRESHOLD = None
-THRESHOLD_PENALTY = 1
-DO_DENSE_REGIONS_DECONVOLUTION = False
-DO_CLUSTER_COMPUTATION = False
-DO_CLUSTER_COMPUTATION = False
-SHOW_NAPARI_CORRECTOR = True
-INTERACTIVE_THRESHOLD = False
-
-#Deconvolution
-ALPHA = 0.5
-BETA = 1.
-GAMMA = 3.
-
-#Clustering
-CLUSTER_SIZE = 400
-MIN_NUMBER_SPOTS = 5
-
-#Coloc
-COLOC_RANGE = 400
-COLOC_VOXEL_SIZE = (1,2,3)
-
-#Spots Extraction
-DO_CSV = False
-DO_EXCEL = False
-SPOT_EXTRACTION_FOLDER = os.getcwd()