phasor-handler 2.2.0__tar.gz

phasor_handler-2.2.0/CONTRIBUTING.md

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+# Contributing to Phasor-Handler
+
+Thanks for your interest in improving Phasor-Handler\! This document explains how to set up a dev environment, coding standards, and how to submit issues/PRs.
+
+> **Platform:** Windows 10/11 only
+> **Primary stack:** Python 3.9, PyQt6, NumPy/SciPy, tifffile/tifftools, Suite2p, Matplotlib
+> **Env manager:** Conda/Mamba (Windows)
+
+-----
+
+## Development Environment Setup
+
+### 1\. Prerequisites
+
+Before you begin, ensure you have the following installed:
+
+  * [Git](https://git-scm.com/downloads)
+  * [Conda](https://www.anaconda.com/products/distribution) (or Miniforge/Mamba for a faster experience)
+
+### 2\. Fork and Clone the Repository
+
+First, create your own copy (a "fork") of the Phasor-Handler repository by clicking the **Fork** button on the GitHub page.
+
+Next, clone your forked repository to your local machine.
+
+```powershell
+# Replace <your-username> with your GitHub username
+git clone https://github.com/<your-username>/Phasor-Handler.git
+
+# Navigate into the project directory
+cd Phasor-Handler
+```
+
+### 3\. Create and Activate the Conda Environment
+
+The `environment.yml` file contains all the necessary dependencies. Create the environment using Mamba (recommended for speed) or Conda.
+
+**Using Mamba:**
+
+```powershell
+mamba env create -f environment.yml
+```
+
+**Or, using Conda:**
+
+```powershell
+conda env create -f environment.yml
+```
+
+Once the installation is complete, activate the new environment. The environment name is specified inside the `.yml` file (let's assume it's `phasor-handler`).
+
+```powershell
+conda activate phasor-handler
+```
+
+### 4\. Install the Application in Editable Mode
+
+To ensure that changes you make to the code are immediately reflected when you run the app, install it in "editable" mode.
+
+```powershell
+# This links the package to your source code
+pip install -e .
+```
+
+### 5\. Run the Application
+
+You are now ready to run the application from the root of the project directory.
+
+```powershell
+python app.py
+```
+
+The application window should now appear. You're all set to start developing\!

phasor_handler-2.2.0/LICENSE.md

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+MIT License
+
+Copyright (c) 2025 Josia Shemuel
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

phasor_handler-2.2.0/MANIFEST.in

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+include README.md
+include LICENSE.md
+include CONTRIBUTING.md
+include environment.yml
+recursive-include img *.ico *.svg
+recursive-include phasor_handler *.py
+global-exclude __pycache__
+global-exclude *.py[co]

phasor_handler-2.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: phasor-handler
+Version: 2.2.0
+Summary: A PyQt6 GUI toolbox for processing two-photon phasor imaging data
+Author-email: Josia Shemuel <joshemuel@users.noreply.github.com>
+License: MIT License
+        
+        Copyright (c) 2025 Josia Shemuel
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+Project-URL: Homepage, https://github.com/joshemuel/Phasor-Handler
+Project-URL: Repository, https://github.com/joshemuel/Phasor-Handler
+Project-URL: Issues, https://github.com/joshemuel/Phasor-Handler/issues
+Keywords: two-photon,phasor,imaging,calcium,neuroscience,suite2p
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Operating System :: Microsoft :: Windows
+Classifier: Environment :: X11 Applications :: Qt
+Requires-Python: <3.10,>=3.9.23
+Description-Content-Type: text/markdown
+License-File: LICENSE.md
+Requires-Dist: PyQt6>=6.4.0
+Requires-Dist: numpy<2.0.0,>=1.21.0
+Requires-Dist: matplotlib>=3.5.0
+Requires-Dist: tifffile>=2021.11.2
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: suite2p>=0.14.0
+Requires-Dist: pyqtdarktheme>=1.0.0
+Requires-Dist: Pillow>=9.0.0
+Requires-Dist: scikit-image>=0.19.0
+Requires-Dist: scipy>=1.7.0
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: black>=22.0.0; extra == "dev"
+Requires-Dist: flake8>=4.0.0; extra == "dev"
+Dynamic: license-file
+
+# Phasor-Handler v2.0 (Windows)
+
+Phasor Handler is a toolbox for processing raw two-photon phasor imaging data: **convert → register → explore → extract calcium traces**.  
+It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.
+
+> ⚠️ **Platform:** Windows 10/11 only  
+> 🧪 Status: actively developed (Brightness & Contrast dialog is WIP)
+
+---
+
+## Features
+
+- Load **registered TIFF** (`Ch1-reg.tif`, `Ch2-reg.tif`) or **raw NPY** fallbacks (`ImageData_Ch0_TP0000000.npy`, `ImageData_Ch1_TP0000000.npy`)
+- Linear and non-linear motion-correct **TIFF images** using Suite2p
+- Automated cell detection using Suite2p
+- Channel switching (Ch1/Ch2) and **Composite (G/R)**
+- **Z-projections**: standard deviation, max, mean
+- **ROI tools**: draw elliptical ROIs, translate or rotate ROIs, save/load as JSON, quick-select saved ROIs
+- **Stimulus overlay**: show stimulated ROI locations from experiment metadata and add to the saved ROIs
+- **Trace plotting**: configurable formula, custom y-limits, frame/time (s) x-axis
+- **Export**: write per-ROI traces for all frames to `.txt` (tab-separated)
+- Keyboard: `R` save/add ROI, `Delete` remove selected ROI, `Esc` clear selection, `Alt+S` load stimulated ROIs, `Right Click + drag` translate selected ROI, `Y` toggle right click to rotation mode
+
+---
+
+## Input data layout
+
+For each dataset directory, Phasor Handler looks for any of:
+
+- Ch1-reg.tif
+- Ch2-reg.tif                 # optional
+- ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
+- ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
+- experiment_summary.pkl      # optional metadata (or .json)
+
+Registered TIFFs are preferred when available; raw NPYs are used as fallback.
+
+---
+
+## Installation (Windows, Conda)
+
+This project provides an `environment.yml` for Windows. The environment is large (GUI, image I/O, napari/suite2p), so **mamba** is recommended, but `conda` works too.
+
+### 1) Install Conda/Mamba (if needed)
+- Install **Miniconda** or **Mambaforge** on Windows.
+- (Optional) Add mamba for faster solves:
+  ```powershell
+  conda install -n base -c conda-forge mamba
+
+### 2) Get the code
+- Clone the repo and change it into
+  ```powershell
+  git clone https://github.com/joshemuel/Phasor-Handler.git
+  chdir Phasor-Handler
+- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
+  cd Phasor-Handler
+
+### 3) Create the environment
+- Using mamba:
+  ```powershell
+  mamba env create -f environment.yml
+- Using conda:
+  ```powershell
+  conda env create -f environment.yml
+
+# 4) Activate and run
+- Before running the toolbox, activate the environment
+  ```powershell
+  conda activate suite2p
+  python app.py
+## Update (Windows, Conda)
+
+### 1) Go to your local repo and pull the latest code from the branch you use
+```powershell
+chdir Phasor-Handler
+git pull --ff-only

phasor_handler-2.2.0/README.md

@@ -0,0 +1,76 @@
+# Phasor-Handler v2.0 (Windows)
+
+Phasor Handler is a toolbox for processing raw two-photon phasor imaging data: **convert → register → explore → extract calcium traces**.  
+It provides a PyQt6 GUI for viewing registered or raw stacks (Ch1/Ch2), z-projections (std/max/mean), drawing/storing ROIs, overlaying stimulated ROIs from metadata, and exporting ROI traces.
+
+> ⚠️ **Platform:** Windows 10/11 only  
+> 🧪 Status: actively developed (Brightness & Contrast dialog is WIP)
+
+---
+
+## Features
+
+- Load **registered TIFF** (`Ch1-reg.tif`, `Ch2-reg.tif`) or **raw NPY** fallbacks (`ImageData_Ch0_TP0000000.npy`, `ImageData_Ch1_TP0000000.npy`)
+- Linear and non-linear motion-correct **TIFF images** using Suite2p
+- Automated cell detection using Suite2p
+- Channel switching (Ch1/Ch2) and **Composite (G/R)**
+- **Z-projections**: standard deviation, max, mean
+- **ROI tools**: draw elliptical ROIs, translate or rotate ROIs, save/load as JSON, quick-select saved ROIs
+- **Stimulus overlay**: show stimulated ROI locations from experiment metadata and add to the saved ROIs
+- **Trace plotting**: configurable formula, custom y-limits, frame/time (s) x-axis
+- **Export**: write per-ROI traces for all frames to `.txt` (tab-separated)
+- Keyboard: `R` save/add ROI, `Delete` remove selected ROI, `Esc` clear selection, `Alt+S` load stimulated ROIs, `Right Click + drag` translate selected ROI, `Y` toggle right click to rotation mode
+
+---
+
+## Input data layout
+
+For each dataset directory, Phasor Handler looks for any of:
+
+- Ch1-reg.tif
+- Ch2-reg.tif                 # optional
+- ImageData_Ch0_TP0000000.npy # raw fallback for Ch1
+- ImageData_Ch1_TP0000000.npy # optional raw fallback for Ch2
+- experiment_summary.pkl      # optional metadata (or .json)
+
+Registered TIFFs are preferred when available; raw NPYs are used as fallback.
+
+---
+
+## Installation (Windows, Conda)
+
+This project provides an `environment.yml` for Windows. The environment is large (GUI, image I/O, napari/suite2p), so **mamba** is recommended, but `conda` works too.
+
+### 1) Install Conda/Mamba (if needed)
+- Install **Miniconda** or **Mambaforge** on Windows.
+- (Optional) Add mamba for faster solves:
+  ```powershell
+  conda install -n base -c conda-forge mamba
+
+### 2) Get the code
+- Clone the repo and change it into
+  ```powershell
+  git clone https://github.com/joshemuel/Phasor-Handler.git
+  chdir Phasor-Handler
+- Alternatively, you can download the entire project as a zip file, unzip it, then open that directory in **Miniconda**
+  cd Phasor-Handler
+
+### 3) Create the environment
+- Using mamba:
+  ```powershell
+  mamba env create -f environment.yml
+- Using conda:
+  ```powershell
+  conda env create -f environment.yml
+
+# 4) Activate and run
+- Before running the toolbox, activate the environment
+  ```powershell
+  conda activate suite2p
+  python app.py
+## Update (Windows, Conda)
+
+### 1) Go to your local repo and pull the latest code from the branch you use
+```powershell
+chdir Phasor-Handler
+git pull --ff-only

phasor_handler-2.2.0/environment.yml

@@ -0,0 +1,219 @@
+name: suite2p
+channels:
+  - conda-forge
+  - defaults
+  - https://repo.anaconda.com/pkgs/main
+  - https://repo.anaconda.com/pkgs/r
+  - https://repo.anaconda.com/pkgs/msys2
+dependencies:
+  - asttokens=3.0.0=pyhd8ed1ab_1
+  - bzip2=1.0.8=h2bbff1b_6
+  - ca-certificates=2025.8.3=h4c7d964_0
+  - colorama=0.4.6=pyhd8ed1ab_1
+  - comm=0.2.3=pyhe01879c_0
+  - cpython=3.9.23=py39hd8ed1ab_0
+  - debugpy=1.8.16=py39h1f3cc84_0
+  - decorator=5.2.1=pyhd8ed1ab_0
+  - exceptiongroup=1.3.0=pyhd8ed1ab_0
+  - executing=2.2.0=pyhd8ed1ab_0
+  - expat=2.7.1=h8ddb27b_0
+  - importlib-metadata=8.7.0=pyhe01879c_1
+  - ipykernel=6.30.1=pyh3521513_0
+  - ipython=8.18.1=pyh7428d3b_3
+  - jedi=0.19.2=pyhd8ed1ab_1
+  - jupyter_client=8.6.3=pyhd8ed1ab_1
+  - jupyter_core=5.8.1=pyh5737063_0
+  - krb5=1.21.3=hdf4eb48_0
+  - libffi=3.4.4=hd77b12b_1
+  - libsodium=1.0.20=hc70643c_0
+  - matplotlib-inline=0.1.7=pyhd8ed1ab_1
+  - nest-asyncio=1.6.0=pyhd8ed1ab_1
+  - openjdk=8.0.412=h57928b3_2
+  - openssl=3.5.2=h725018a_0
+  - packaging=25.0=pyh29332c3_1
+  - parso=0.8.4=pyhd8ed1ab_1
+  - pickleshare=0.7.5=pyhd8ed1ab_1004
+  - pip=25.1=pyhc872135_2
+  - platformdirs=4.3.8=pyhe01879c_0
+  - prompt-toolkit=3.0.51=pyha770c72_0
+  - psutil=7.0.0=py39ha55e580_0
+  - pure_eval=0.2.3=pyhd8ed1ab_1
+  - pygments=2.19.2=pyhd8ed1ab_0
+  - python=3.9.23=h716150d_0
+  - python-dateutil=2.9.0.post0=pyhe01879c_2
+  - python_abi=3.9=2_cp39
+  - pywin32=311=py39h5fb4b08_0
+  - pyzmq=27.0.1=py39h248659b_0
+  - setuptools=78.1.1=py39haa95532_0
+  - six=1.17.0=pyhe01879c_1
+  - sqlite=3.50.2=hda9a48d_1
+  - stack_data=0.6.3=pyhd8ed1ab_1
+  - tk=8.6.15=hf199647_0
+  - tornado=6.5.2=py39h0802e32_0
+  - traitlets=5.14.3=pyhd8ed1ab_1
+  - typing_extensions=4.14.1=pyhe01879c_0
+  - ucrt=10.0.22621.0=haa95532_0
+  - vc=14.3=h2df5915_10
+  - vc14_runtime=14.44.35208=h4927774_10
+  - vs2015_runtime=14.44.35208=ha6b5a95_10
+  - wcwidth=0.2.13=pyhd8ed1ab_1
+  - wheel=0.45.1=py39haa95532_0
+  - xz=5.6.4=h4754444_1
+  - zeromq=4.3.5=ha9f60a1_7
+  - zipp=3.23.0=pyhd8ed1ab_0
+  - zlib=1.2.13=h8cc25b3_1
+  - pip:
+      - alabaster==0.7.16
+      - annotated-types==0.7.0
+      - app-model==0.3.2
+      - appdirs==1.4.4
+      - attrs==25.3.0
+      - babel==2.17.0
+      - bcrypt==4.3.0
+      - build==1.3.0
+      - cachey==0.2.1
+      - cellpose==3.1.1.2
+      - certifi==2025.8.3
+      - cffi==1.17.1
+      - charset-normalizer==3.4.3
+      - cjdk==0.4.1
+      - click==8.1.8
+      - cloudpickle==3.1.1
+      - contourpy==1.3.0
+      - cryptography==45.0.6
+      - cycler==0.12.1
+      - darkdetect==0.7.1
+      - dask==2024.8.0
+      - dcimg==0.6.0.post1
+      - docstring-parser==0.17.0
+      - docutils==0.21.2
+      - fastremap==1.17.2
+      - filelock==3.19.1
+      - fill-voids==2.1.0
+      - flexcache==0.3
+      - flexparser==0.4
+      - fonttools==4.59.1
+      - freetype-py==2.5.1
+      - fsspec==2025.7.0
+      - h5py==3.14.0
+      - hdmf==4.1.0
+      - heapdict==1.0.1
+      - hsluv==5.0.4
+      - idna==3.10
+      - ij==0.0.6
+      - imagecodecs==2024.12.30
+      - imageio==2.37.0
+      - imagesize==1.4.1
+      - imglyb==2.1.0
+      - importlib-resources==6.5.2
+      - in-n-out==0.2.1
+      - invoke==2.2.0
+      - ipywidgets==8.1.7
+      - jgo==1.0.6
+      - jinja2==3.1.6
+      - joblib==1.5.1
+      - jpype1==1.6.0
+      - jsonschema==4.25.1
+      - jsonschema-specifications==2025.4.1
+      - jupyterlab-widgets==3.0.15
+      - kiwisolver==1.4.7
+      - labeling==0.1.14
+      - lazy-loader==0.4
+      - llvmlite==0.43.0
+      - locket==1.0.0
+      - magicgui==0.10.1
+      - markdown-it-py==3.0.0
+      - markupsafe==3.0.2
+      - matplotlib==3.9.4
+      - mdurl==0.1.2
+      - mpmath==1.3.0
+      - napari==0.5.6
+      - napari-console==0.1.3
+      - napari-plugin-engine==0.2.0
+      - napari-svg==0.2.1
+      - natsort==8.4.0
+      - nd2==0.10.3
+      - networkx==3.2.1
+      - npe2==0.7.9
+      - numba==0.60.0
+      - numpy==2.0.2
+      - numpydoc==1.9.0
+      - ome-types==0.6.1
+      - opencv-python-headless==4.12.0.88
+      - pandas==2.3.1
+      - paramiko==4.0.0
+      - partd==1.4.2
+      - pillow==11.3.0
+      - pint==0.24.4
+      - pooch==1.8.2
+      - progressbar2==4.5.0
+      - psygnal==0.14.1
+      - pyconify==0.2.1
+      - pycparser==2.22
+      - pydantic==2.11.7
+      - pydantic-compat==0.1.2
+      - pydantic-core==2.33.2
+      - pydantic-extra-types==2.10.5
+      - pyimagej==1.7.0
+      - pynacl==1.5.0
+      - pynwb==3.1.2
+      - pyopengl==3.1.10
+      - pyparsing==3.2.3
+      - pyproject-hooks==1.2.0
+      - pyqt6==6.9.1
+      - pyqt6-qt6==6.9.1
+      - pyqt6-sip==13.10.2
+      - pyqtdarktheme==2.1.0
+      - pyqtgraph==0.13.7
+      - python-utils==3.9.1
+      - pytz==2025.2
+      - pyyaml==6.0.2
+      - qdarkstyle==3.2.3
+      - qtconsole==5.6.1
+      - qtpy==2.4.3
+      - rastermap==1.0
+      - referencing==0.36.2
+      - requests==2.32.5
+      - resource-backed-dask-array==0.1.0
+      - rich==14.1.0
+      - roifile==2024.9.15
+      - rpds-py==0.27.0
+      - ruamel-yaml==0.18.15
+      - ruamel-yaml-clib==0.2.12
+      - sbxreader==0.2.2
+      - scanimage-tiff-reader==1.4.1.4
+      - scikit-image==0.24.0
+      - scikit-learn==1.6.1
+      - scipy==1.13.1
+      - scyjava==1.12.1
+      - shellingham==1.5.4
+      - snowballstemmer==3.0.1
+      - sphinx==7.4.7
+      - sphinxcontrib-applehelp==2.0.0
+      - sphinxcontrib-devhelp==2.0.0
+      - sphinxcontrib-htmlhelp==2.1.0
+      - sphinxcontrib-jsmath==1.0.1
+      - sphinxcontrib-qthelp==2.0.0
+      - sphinxcontrib-serializinghtml==2.0.0
+      - suite2p==0.14.5
+      - superqt==0.7.6
+      - sympy==1.14.0
+      - threadpoolctl==3.6.0
+      - tifffile==2024.8.30
+      - tifftools==1.6.1
+      - tomli==2.2.1
+      - tomli-w==1.2.0
+      - toolz==1.0.0
+      - torch==2.8.0
+      - tqdm==4.67.1
+      - typer==0.17.4
+      - typing-inspection==0.4.1
+      - tzdata==2025.2
+      - urllib3==2.5.0
+      - vispy==0.14.3
+      - widgetsnbextension==4.0.14
+      - wrapt==1.17.3
+      - xarray==2024.7.0
+      - xmltodict==0.14.2
+      - xsdata==24.3.1
+prefix: C:\Users\user\anaconda3\envs\suite2p

phasor_handler-2.2.0/img/icons/chevron-down.svg

@@ -0,0 +1,3 @@
+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24">
+  <path fill="white" d="M7.41 8.59L12 13.17l4.59-4.58L18 10l-6 6-6-6z"/>
+</svg>

phasor_handler-2.2.0/img/icons/chevron-up.svg

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+<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24">
+  <path fill="white" d="M7.41 15.41L12 10.83l4.59 4.58L18 14l-6-6-6 6z"/>
+</svg>

phasor_handler-2.2.0/phasor_handler/__init__.py

@@ -0,0 +1,9 @@
+"""
+Phasor Handler - Two-Photon Phasor Imaging Data Processor
+
+A PyQt6 GUI toolbox for processing two-photon phasor imaging data.
+"""
+
+__version__ = "2.2.0"
+__author__ = "Josia Shemuel"
+__all__ = ["app", "widgets", "workers", "models", "scripts", "tools", "themes"]