Fix tif pool scatter imports

.gitignore

@@ -1,3 +1,10 @@
+*.egg-info
+.coverage*
+.vscode/
+data/
+pyinstaller/macos/_secrets.py
+sandbox/
+
 pyinstaller/monterey/tmp_env
 
 build/
@@ -8,6 +15,10 @@ sanpy_env/*
 sanpy.log
 sanpy/sanpy.log
 
+# Log files
+logs/
+*.log
+
 .AppleDouble
 .DS_Store
 *.pyc

CHANGELOG.md

@@ -1,6 +1,19 @@
 
 SanPy Documentation is available at [https://cudmore.github.io/SanPy/](https://cudmore.github.io/SanPy/)
 
+## 202403
+
+### New features
+
+ - Re-added the File - Save menu. This will save the current analysis for one file or a folder.
+ - Added a "bin time" pooling option to summary plugin. Makes a table with stats (count, mean, std, se, median) in evenly spaced windows of time. For example pooles between [0,2) then [2,4) then [4,6), etc,  seconds.
+ - Added a colorbar to scatter plot plugin when selecting hue as "Time". This allows users to know where a point in the scatter occured in the recording time.
+
+### Bug fixes
+
+ - Fixed bug in plugin - summarize results - sweep summary
+ - Fixed bug in plugin - plot scatter when selecting hue of Time or Sweep
+
 ## 20240126
 
  - Added a file folder opening window. This is show at first run and allows users to open new and previous opened files and folder.

dev-notes/colin-dev-log.md

@@ -0,0 +1,36 @@
+# Colin Development Log
+
+This file tracks ongoing development, refactoring, and testing for colin-related code in the SanPy project.
+
+**Note:** This development log was mostly auto-generated by Cursor AI, an AI coding assistant, to help track changes and maintain context during development.
+
+---
+
+## 2024-06-13: Refactor, Utility Improvements, and Robust Testing
+
+### Major Changes
+- **Refactored** `colin_global.py` and `colin_stats.py` for clarity, maintainability, and best practices.
+- **Introduced** the `FileInfo` dataclass for robust parsing of file paths (e.g., extracting cellID, epoch, date, region, condition).
+- **Added** a utility iterator function to return unique rows for a given cellID from a DataFrame.
+- **Replaced** ad-hoc file parsing logic in `colin_stats.py` with the new `FileInfo` dataclass.
+- **Fixed** pandas `SettingWithCopyWarning` by using `.copy()` when needed.
+
+### Testing
+- **Created** `sanpy/kym/tests/test_colin_global.py` and `test_colin_stats.py`:
+  - Each test prints results and uses `assert` statements to verify expected values.
+  - Tests cover normal cases, edge cases, and error conditions.
+  - Tests for DataFrame operations, iterator logic, and `.copy()` best practices.
+- **Added** `run_all_tests.py` to run all colin-related tests and provide a summary.
+- **Added** a `README.md` in the tests folder to document test structure and usage.
+
+### Benefits
+- **Regression-proof**: Tests will catch breaking changes or regressions.
+- **Documentation**: Test cases and this log serve as living documentation.
+- **Maintainability**: Refactored code is easier to extend and debug.
+- **Professional structure**: Follows best practices for code and test organization.
+
+---
+
+**Next Steps:**
+- Continue to log all major refactors, new utilities, and test improvements here.
+- Use this file for context when returning to the project or onboarding collaborators. 

pyinstaller/macos/build_arm.sh

@@ -64,7 +64,14 @@ conda install -y numpy \
 conda install -y -c conda-forge mplcursors
 
 pip install pyabf
+
+# 20250627, abb building sanpykym, we might need, pyqtdarktheme-fork
 pip install pyqtdarktheme
+pip install qtawesome
+pip install roifile
+pip install statannotations
+# pip install tifffile
+# pip install tables
 
 # install sanpy with no packages
 pip install -e '../../.'
@@ -76,4 +83,5 @@ pip install pyinstaller
 # build the app with pyinstaller
 python macos_build.py
 
-python notarizeSanpy.py dist_arm
+# abb 202506 turn back on to notarize, getting password error
+# python notarizeSanpy.py dist_arm

pyinstaller/macos/readme.md

@@ -1,5 +1,7 @@
 This folder contains scripts to build macOS app(s) from Python source code using pyinstaller.
 
+My apple developer account is at https://developer.apple.com/account
+
 Building a Python app on macOS is by no means simple. The app needs to be properly codesigned, notarized on an Apple server (requires uploading a zip of the app to Apple), waiting for the ok, and then staple(ing) the app with the notarization.
 
 This all requires an Apple Developer Subscription which is $99/year.

pyproject.toml

@@ -2,9 +2,67 @@
 requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
 build-backend = "setuptools.build_meta"
 
-#[project]
+[project]
+name = "sanpy"
 # version = "0.0.1"  # Remove any existing version parameter.
-#dynamic = ["version"]
+dynamic = ["version"]
+requires-python = ">=3.11"
+dependencies = []  # Base install has no requirements
+
+[project.optional-dependencies]
+gui = [
+    "h5py",
+    "matplotlib",
+    "mplcursors",
+    "numpy>=1.20.0",
+    "pandas>=2.0.0",
+    "pyabf",
+    "PyQt5>=5.15.0",
+    "pyqtdarktheme-fork",
+    "pyqtgraph",
+    "qtawesome",
+    "qtpy",
+    "requests",
+    "roifile",  # For reading Fiji ROI files
+    "scikit-image",
+    "scipy>=1.8.0",
+    "seaborn",  # For statistical visualizations
+    "statannotations",  # For statistical annotations
+    "tables",
+    "tifffile"
+]
+
+dev = [
+    "flake8",
+    "ipython",
+    "jupyter",
+    "mkdocs",
+    "mkdocs-material", 
+    "mkdocs-jupyter",
+    "mkdocstrings",
+    "mkdocstrings-python",
+    "pyinstaller",
+    "pytest",
+    "pytest-cov",
+    "pytest-qt",
+    "tornado",
+    "tox"
+]
+
+test = [
+    "flake8",
+    "pytest",
+    "pytest-cov", 
+    "pytest-qt",
+    "tox"
+]
+
+[project.scripts]
+sanpy = "sanpy.interface.sanpy_app:main"
+sanpykym = "sanpy.kym.interface.kym_file_list.tif_tree_window:main"
+
+[tool.setuptools]
+packages = ["sanpy"]
 
 [tool.setuptools_scm]
 write_to = "sanpy/_version.py"
@@ -15,4 +73,7 @@ local_scheme = "no-local-version"
 [tool.ruff]
 ignore = [
     "E501",  # Supress line-too-long warnings: trust black's judgement on this one.
-]
+]
+
+[tool.pytest.ini_options]
+addopts = "--ignore=napari"

readme-dev.md

@@ -30,6 +30,32 @@ git tag -d v0.1.25
 git push --delete origin v0.1.25
 ``` 
 
+202402
+
+list remote tags
+    git ls-remote --tags origin  
+commit with a tag
+    git tag -a v1.0.36 -m 'release 1.0.36'
+push the tag
+    git push --follow-tags   
+
+get version from setup
+    python setup.py --version
+
+I AM SO SICK OF VERSIONING !!!!!!
+
+Logic is (this is the way)
+
+```
+update version in setup.py
+update version in _myVersion.py
+git commit -am 'v1.0.42'
+git push
+
+git tag -a v1.0.42 -m 'release v1.0.42'
+git push --follow-tags     
+```
+
 ## Lock down a version to accompany SanPy manuscript
 
 Working on publishing v0.1.8

sanpy/__init__.py

@@ -1,6 +1,6 @@
 # using this to turn off for 1st sanpy publication
-D_BJ_MANUSCRIPT = True
-DO_KYMOGRAPH_ANALYSIS = False
+D_BJ_MANUSCRIPT = False
+DO_KYMOGRAPH_ANALYSIS = True
 
 from .sanpyLogger import *
 

sanpy/_util.py

@@ -200,6 +200,26 @@ def _loadLineScanHeader(path):
 
     txtFile = os.path.splitext(path)[0] + ".txt"
 
+    if not os.path.isfile(txtFile):
+        # find "ISAN Linescan 6 Metadata.txt"
+        logger.info(f'did not find {txtFile}')
+        logger.info('  -->> searching ...')
+
+        _folder, _file = os.path.split(path)
+        _file, _ = os.path.splitext(_file)
+        _file += ' Metadata.txt'
+        logger.info(f'   -->> looking for Olympus "{_file}"')
+        txtFile = os.path.join(_folder, _file)
+        if not os.path.isfile(txtFile):
+            _folder, _file = os.path.split(path)
+            _file, _ = os.path.splitext(_file)
+            _file = _file.split('_')[0]  # may fail
+            _file += '.txt'
+            logger.info(f'     -->> looking for Olympus "{_file}"')
+            txtFile = os.path.join(_folder, _file)
+            if not os.path.isfile(txtFile):
+                logger.warning(f'DID NOT FIND CORRESPONDING OLYMPUS FILE: {os.path.split(path)[1]}')
+
     if not os.path.isfile(txtFile):
         # logger.error(f"did not find file:{txtFile}")
 
@@ -283,6 +303,17 @@ def _loadLineScanHeader(path):
             # elif line.startswith('"Image Size(Unit Converted)"'):
             # 	print('loadLineScanHeader:', line)
 
+            elif line.startswith('"Date"'):
+                # "Date"	"09/12/2024 01:33:26.239 PM"
+                # logger.info(f'date line is: {line}')
+                _date, _datetime = line.split('\t')
+                _datetime = _datetime.replace('"', '')  # remove ""
+                _date, _time, _ampm = _datetime.split(' ')
+                # logger.info(f'   _date:{_date} _time:{_time} _ampm:{_ampm}')
+
+                theRet ['date'] = _date
+                theRet ['time'] = _time + ' ' + _ampm
+
     # tif shape is (lines, pixels)
     if gotNumPixels and gotImageSize:
         shape = (theRet["numLines"], theRet["numPixels"])
@@ -341,9 +372,5 @@ def getFileList(path, depth=1):
     return fileList
 
 if __name__ == '__main__':
-    path = '/Users/cudmore/Dropbox/data/cell-shortening/fig1'
-    fileList = getFileList(path, 4)
-    for file in fileList:
-        print(file)
-
+    pass