dev into master

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/api/extensions.rst

@@ -0,0 +1,111 @@
+Caiman Extensions
+*****************
+
+Pandas extensions for CaImAn functionality with DataFrames.
+
+Common
+======
+
+Extensions that are used for both MCorr (motion correction) and CNMF(E)
+
+.. autoclass:: mesmerize_core.CaimanDataFrameExtensions
+    :members: 
+
+.. autoclass:: mesmerize_core.CaimanSeriesExtensions
+    :members:
+
+MCorr
+=====
+
+Extensions that are exlusive to motion correction
+
+.. autoclass:: mesmerize_core.MCorrExtensions
+    :members:
+
+
+CNMF
+====
+
+.. autoclass:: mesmerize_core.CNMFExtensions
+    :members:
+
+Example
+=======
+
+.. code-block:: python
+
+    from mesmerize_core import COMPUTE_BACKENDS, COMPUTE_BACKEND_QPROCESS, COMPUTE_BACKEND_SLURM, \
+    COMPUTE_BACKEND_SUBPROCESS, set_parent_data_path, get_parent_data_path, get_full_data_path, \
+    load_batch, create_batch
+    from mesmerize_core.caiman_extensions import *
+
+    # set the parent directory as the top-level directory for your experiment data
+    set_parent_data_path('/home/kushal/my_exps_dir')
+
+    batch_path = '/home/kushal/my_exps_dir/my_batches/exp_1_batch.pickle'
+
+    # create a new batch
+    df = create_batch(batch_path)
+
+    # path to raw movie tiff file
+    movie_path = '/home/kushal/my_exps_dir/exp_1/my_movie.tif'
+
+    # params, exactly the same as what you'd directly use with CaImAn
+    mcorr_params1 = 
+    {
+    'mcorr_kwargs': # this key is necessary for specifying that these are mcorr kwargs
+        {
+            'max_shifts': [24, 24],
+            'strides': [48, 48],
+            'overlaps': [24, 24],
+            'max_deviation_rigid': 3,
+            'border_nan': 'copy',
+            'pw_rigid': True,
+            'gSig_filt': None
+        },
+    }
+
+    df.caiman.add_item(
+    algo='mcorr',
+    name='my_movie',
+    input_movie_path=movie_path,
+    params=mcorr_params1
+    )
+
+    # We create another set of params, useful for gridsearches for example
+    mcorr_params2 =\ 
+    {
+    'mcorr_kwargs': # this key is necessary for specifying that these are mcorr kwargs
+        {
+            'max_shifts': [24, 24],
+            'strides': [24, 24],
+            'overlaps': [12, 12],
+            'max_deviation_rigid': 3,
+            'border_nan': 'copy',
+            'pw_rigid': True,
+            'gSig_filt': None
+        },
+    }
+
+    df.caiman.add_item(
+    algo='mcorr',
+    name='my_movie',
+    input_movie_path=movie_path,
+    params=mcorr_params2
+    )
+
+    # run the first "batch item"
+    process = df.iloc[0].caiman.run(
+    batch_path=batch_path,
+    backend=COMPUTE_BACKEND_SUBPROCESS,  # this is for non-GUI use, COMPUTE_BACKEND_QPROCESS is for use within a Qt GUI
+    callbacks_finished=[lambda: print("yay finished")], # callback function for when this item finishes
+    )
+
+    # run the second item
+    # you can also use a loop to run all these items
+    # just call process.wait() to run them one after another
+    process = df.iloc[1].caiman.run(
+    batch_path=batch_path,
+    backend=COMPUTE_BACKEND_SUBPROCESS,
+    callbacks_finished=[lambda: print("yay finished")],
+    )

docs/source/conf.py

@@ -0,0 +1,54 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'mesmerize-core'
+copyright = '2022, Kushal Kolar, Arjun Putcha, Caitlin Lewis'
+author = 'Kushal Kolar, Arjun Putcha, Caitlin Lewis'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ["sphinx.ext.napoleon"]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/index.rst

@@ -0,0 +1,23 @@
+.. mesmerize-core documentation master file, created by
+   sphinx-quickstart on Wed Jun  1 17:14:50 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to mesmerize-core's documentation!
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   ./api/extensions
+
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

mesmerize_core/caiman_extensions/cnmf.py

@@ -69,7 +69,6 @@ def get_output_path(self) -> Path:
         """
         return get_full_data_path(self._series["outputs"]["cnmf-hdf5-path"])
 
-    # @lru_cache(MESMERIZE_LRU_CACHE)
     @validate("cnmf")
     def get_output(self) -> CNMF:
         """
@@ -129,7 +128,6 @@ def get_spatial_masks(
 
     # TODO: Cache this globally so that a common upper cache limit is valid for ALL batch items
     @staticmethod
-    @lru_cache(5)
     def _get_spatial_contours(
         cnmf_obj: CNMF, ixs_components: Optional[np.ndarray] = None
     ):