monochrome 2024.3.6__tar.gz → 2024.3.21__tar.gz

{monochrome-2024.3.6/monochrome_viewer.egg-info → monochrome-2024.3.21}/PKG-INFO

@@ -1,11 +1,8 @@
 Metadata-Version: 2.1
 Name: monochrome
-Version: 2024.3.6
-Summary: Viewer for scientific monochromatic video data
-Home-page: https://gitlab.com/sitic/monochrome
-Author: Jan Lebert
-Author-email: mail@janlebert.com
-License: MIT
+Version: 2024.3.21
+Summary: Viewer for monochromatic video data
+Author-Email: Jan Lebert <mail@janlebert.com>
 Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: MIT License
@@ -17,12 +14,12 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Desktop Environment
 Classifier: Topic :: Multimedia :: Video :: Display
 Classifier: Topic :: Scientific/Engineering :: Visualization
+Project-URL: Documentation, https://monochrome.readthedocs.io
+Project-URL: Repository, https://github.com/sitic/monochrome
 Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE.md
 Requires-Dist: numpy
 Requires-Dist: flatbuffers>=23.5.26
-Provides-Extra: docs
+Requires-Dist: pytest; extra == "test"
 Requires-Dist: sphinx; extra == "docs"
 Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
 Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
@@ -38,6 +35,9 @@ Requires-Dist: sphinx-remove-toctrees; extra == "docs"
 Requires-Dist: sphinx-design; extra == "docs"
 Requires-Dist: enum-tools[sphinx]; extra == "docs"
 Requires-Dist: opticalmapping[all]; extra == "docs"
+Provides-Extra: test
+Provides-Extra: docs
+Description-Content-Type: text/markdown
 
 # Monochrome: Viewer for Monochromatic Video Data
 [![docs](https://readthedocs.org/projects/monochrome/badge/?version=latest&style=)](https://monochrome.readthedocs.org)

monochrome-2024.3.21/pyproject.toml

@@ -0,0 +1,100 @@
+[build-system]
+requires = [
+    "scikit-build-core",
+    "setuptools_scm>=6.2",
+]
+build-backend = "scikit_build_core.build"
+
+[project]
+name = "monochrome"
+dynamic = ["version"]
+description="Viewer for monochromatic video data"
+readme = "README.md"
+requires-python = ">=3.6"
+authors = [
+    {name = "Jan Lebert", email = "mail@janlebert.com" }
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: Microsoft :: Windows",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX",
+    "Programming Language :: C++",
+    "Programming Language :: Python :: 3",
+    "Topic :: Desktop Environment",
+    "Topic :: Multimedia :: Video :: Display",
+    "Topic :: Scientific/Engineering :: Visualization",
+]
+dependencies = [
+    "numpy",
+    "flatbuffers>=23.5.26"
+]
+
+[project.urls]
+Documentation = "https://monochrome.readthedocs.io"
+Repository = "https://github.com/sitic/monochrome"
+
+[project.optional-dependencies]
+test = [
+    "pytest"
+]
+"docs" = [
+    "sphinx",
+    "sphinxcontrib-napoleon",
+    "sphinxcontrib-bibtex",
+    "sphinxcontrib-video",
+    "sphinx-autobuild",
+    "sphinx-copybutton",
+    "sphinx-codeautolink",
+    "furo",
+    "myst_nb>=1.0.0",
+    "jupytext",
+    "jupyter-cache",
+    "sphinx-remove-toctrees",
+    "sphinx-design",
+    "enum-tools[sphinx]",
+    "opticalmapping[all]"
+]
+
+[project.gui-scripts]
+Monochrome = "monochrome.ipc:console_entrypoint"
+
+[tool.scikit-build]
+metadata.version.provider = "scikit_build_core.metadata.setuptools_scm"
+sdist.include = ["src/python/monochrome/_version.py"]
+cmake.version = ">=3.12"
+cmake.verbose = true
+cmake.args = [
+        "-DSTATIC_GCC:BOOL=ON",
+        "-DDISABLE_MACOS_BUNDLE:BOOL=ON",
+]
+wheel.packages = [ "src/python/monochrome" ]
+wheel.py-api = "py3"
+wheel.install-dir = "monochrome/data"
+
+[tool.scikit-build.cmake.define]
+STATIC_GCC = "ON"
+DISABLE_MACOS_BUNDLE = "ON"
+
+[tool.setuptools_scm]
+write_to = "src/python/monochrome/_version.py"
+fallback_version = "0.1"
+
+[tool.pytest.ini_options]
+testpaths = "src/python/tests"
+
+[tool.cibuildwheel]
+archs = ["auto64"]  # 64-bit only
+skip = "pp* *musllinux*"  # disable PyPy, musl-based wheels
+test-requires = ["pytest"]
+test-command = "pytest {project}/src/python/tests"
+
+[tool.cibuildwheel.macos]
+# https://cibuildwheel.readthedocs.io/en/stable/faq/#apple-silicon
+archs = ["universal2"]
+test-skip = ["*_arm64", "*_universal2:arm64"]
+
+[tool.cibuildwheel.linux]
+before-all = "yum install -y libXrandr-devel libXcursor-devel libXinerama-devel libXi-devel mesa-libGL-devel libdwarf-devel binutils-devel"

{monochrome-2024.3.6 → monochrome-2024.3.21}/src/cpp/utils/videorecorder.h

@@ -96,7 +96,7 @@ class VideoRecorder {
     buffer = std::vector<GLubyte>(width * height * 3ul);
 
     std::string cmd = fmt::format(
-        "\"{ffmpeg_exe}\" -f rawvideo -pix_fmt rgb24 -framerate {fps:d} "
+        "{ffmpeg_exe} -f rawvideo -pix_fmt rgb24 -framerate {fps:d} "
         "-video_size {width}x{height} -i - -y -threads 0 {encoder_args} -pix_fmt yuv420p "
         // ensure height and width are divisible by 2
         "-vf \"[in]vflip,scale=trunc(iw/2)*2:trunc(ih/2)*2[out]\" "

{monochrome-2024.3.6 → monochrome-2024.3.21}/src/python/monochrome/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '2024.3.6'
-__version_tuple__ = version_tuple = (2024, 3, 6)
+__version__ = version = '2024.3.21'
+__version_tuple__ = version_tuple = (2024, 3, 21)

monochrome-2024.3.6/PKG-INFO

@@ -1,163 +0,0 @@
-Metadata-Version: 2.1
-Name: monochrome
-Version: 2024.3.6
-Summary: Viewer for scientific monochromatic video data
-Home-page: https://gitlab.com/sitic/monochrome
-Author: Jan Lebert
-Author-email: mail@janlebert.com
-License: MIT
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: Microsoft :: Windows
-Classifier: Operating System :: MacOS
-Classifier: Operating System :: POSIX
-Classifier: Programming Language :: C++
-Classifier: Programming Language :: Python :: 3
-Classifier: Topic :: Desktop Environment
-Classifier: Topic :: Multimedia :: Video :: Display
-Classifier: Topic :: Scientific/Engineering :: Visualization
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE.md
-Requires-Dist: numpy
-Requires-Dist: flatbuffers>=23.5.26
-Provides-Extra: docs
-Requires-Dist: sphinx; extra == "docs"
-Requires-Dist: sphinxcontrib-napoleon; extra == "docs"
-Requires-Dist: sphinxcontrib-bibtex; extra == "docs"
-Requires-Dist: sphinxcontrib-video; extra == "docs"
-Requires-Dist: sphinx-autobuild; extra == "docs"
-Requires-Dist: sphinx-copybutton; extra == "docs"
-Requires-Dist: sphinx-codeautolink; extra == "docs"
-Requires-Dist: furo; extra == "docs"
-Requires-Dist: myst_nb>=1.0.0; extra == "docs"
-Requires-Dist: jupytext; extra == "docs"
-Requires-Dist: jupyter-cache; extra == "docs"
-Requires-Dist: sphinx-remove-toctrees; extra == "docs"
-Requires-Dist: sphinx-design; extra == "docs"
-Requires-Dist: enum-tools[sphinx]; extra == "docs"
-Requires-Dist: opticalmapping[all]; extra == "docs"
-
-# Monochrome: Viewer for Monochromatic Video Data
-[![docs](https://readthedocs.org/projects/monochrome/badge/?version=latest&style=)](https://monochrome.readthedocs.org)
-[![tests](https://github.com/sitic/monochrome/actions/workflows/build.yml/badge.svg)](https://github.com/sitic/monochrome/actions/workflows/build.yml)
-[![PyPI](https://img.shields.io/pypi/v/monochrome.svg)](https://pypi.org/project/monochrome/)
-[![Supported Python versions](https://img.shields.io/pypi/pyversions/monochrome.svg)](https://python.org)
-
-Monochrome is a lightweight and fast video viewer for scientific monochromatic videos with high-dynamic range (float, uint16, etc.).
-
-It is designed for viewing high-speed monochromatic fluorescence video data from scientific cameras and meet our specific needs for cardiac optical mapping data (together with [optimap](https://github.com/cardiacvision/optimap)):
-* Support for high-dynamic range (uint16, 32-bit float) data with sliders to adjust intensity range
-* Playback of multiple videos in sync
-* High-speed playback with precise frame-rate control
-* Viewing of optical traces (average intensity in a region of interest over time)
-* Rendering of layers on top of videos with transparency
-* Rendering of point positions over time (e.g. for tracking or optical flow visualization)
-* Exporting videos as a sequence of PNG images or MP4 videos with control over frame rate and frame skipping
-* Cross-platform (Linux, Windows, MacOS)
-
-It is designed to be fast and lightweight, i.e. it uses memory-mapping to load video files to avoid copying the data into RAM.
-
-## Installation
-
-There are two ways to install Monochrome: as a standalone application and/or with its Python interface through pip.
-
-In the standalone application, supported video files can be loaded by drag & drop them into the window or by associating the file extension with Monochrome to open them with a double-click. The Python interface allows to load and play videos from Python scripts and Jupyter notebooks.
-
-### Standalone Application
-
-Download the relevant executable (Windows, macOS, or Linux) from the latest [release page](https://github.com/sitic/monochrome/releases/latest). See the [installation instructions](https://monochrome.readthedocs.io/latest/installation_standalone/) for details.
-
-### Python Library
-
-The Python library includes all necessary files and does not require the installation of the standalone Monochrome application. Open a terminal window and run the following command:
-
-```bash
-python -m pip install monochrome
-```
-
-See the [Python installation guide](https://monochrome.readthedocs.io/latest/installation_python/) for further details. To start the viewer in standalone mode, run:
-```bash
-python -m monochrome
-```
-
-See the [tutorial](https://monochrome.readthedocs.io/latest/tutorial/) for an introduction to the Python library, here is a brief overview:
-
-```python
-import monochrome as mc
-import numpy as np
-
-# Create some video with shape (time, height, width) as a numpy array
-video = np.random.rand(500, 256, 256)
-
-# Display the video, see the tutorial for more details and options.
-# Monochrome should automatically start and show the video in a loop.
-mc.show_video(video, name="First Video", cmap='viridis', vmin=0, vmax=1)
-
-# Play second video in sync with the first (note that the videos should have the same length)
-video2 = (np.random.rand(500, 256, 256) * 65535).astype(dtype=np.uint16)
-mc.show_video(video2, name="Second Video", comment="This is a uint16 video", bitrange="uint16")
-# `bitrange` argument is optional, Monochrome will auto-detect the data type
-
-# Layers can be added on top of video
-overlay = np.random.rand(500, 256, 256)
-overlay[:, 64:192, :] = np.nan # NaN values will be transparent pixels, see tutorial
-mc.show_layer(overlay, parent="Second Video", cmap='PRGn', opacity='centered')
-
-# List of functions:
-# mc.show() is a shortcut for mc.show_video()/show_layer()/show_image()/show_file(),
-#           it will try to auto-detect the input type and call the appropriate function.
-# mc.show_video() to show videos
-# mc.show_image() to show single images
-# mc.show_layer() to show layers on top of videos/images
-# mc.show_points() to visualize point positions over time over videos
-# mc.show_flow() to visualize optical flow fields over time
-# mc.show_file() to load videos from file in Monochrome
-# mc.launch() to start Monochrome from Python
-```
-
-## Native Video File Formats
-Monochrome supports loading the following video file formats:
-
-* `.npy`, NumPy array with shape (time, width, height). The data type can be float (np.float32, np.float64), integer (uint8, uint16, etc.), or boolean.
-* `.dat`, raw binary file with shape (time, width, height) and data type float32
-* `.dat`, MultiRecorder file format (used in the cardiac optical mapping community)
-
-Drag & drop the file into the window or associate the file extension with Monochrome to open it with a double-click.
-
-## Usage & Key Bindings
-
-Adjust settings for each video in the main control window. To view optical traces (average intensity in a region of interest over time), click in a video. Click and drag to move the region of interest. Right-click to remove the region of interest.
-
-Keyboard shortcuts:
-
-| Keybinding         | Action                |
-| --- | --- |
-| `Ctrl + q` | Quit Monochrome |
-| `Esc` or `q` | Close focused recording |
-| `Space` | Play/Pause |
-| `Up` | Increase playback speed (frame skip) |
-| `Down` | Decrease playback speed (frame skip) |
-| `0` or `r` | Reset playback to beginning |
-| `Left` | Skip to next frame |
-| `Right` | Skip to previous frame |
-| `Shift + Left` | 10x previous frame |
-| `Shift + Right` | 10x next frame |
-| `Ctrl + Left` | Previous frame in focused recording only |
-| `Ctrl + Right` | Next frame in focused recording only |
-| `Ctrl + Left + Shift` | 10x previous frame in focused recording only |
-| `Ctrl + Right + Shift` | 10x next frame in focused recording only |
-| `p` | Save screenshot of focused recording |
-| `s` | Sync playback of all recordings |
-
-## Additional Resources
-
-* [Documentation](https://monochrome.readthedocs.io)
-* [Python Tutorial](https://monochrome.readthedocs.io/latest/tutorial/)
-* [PyPI package](https://pypi.org/project/monochrome/)
-* [GitHub repository](https://github.com/sitic/monochrome)
-
-## License
-
-Monochrome is licensed under the MIT License.