Merge pull request #41 from kabilar/main

Update `suite2p_trigger` documentation

Author: tdincer

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,39 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: 'bug'
+assignees: ''
+
+---
+
+## Bug Report
+
+### Description
+
+A clear and concise description of what is the overall operation that is intended to be
+performed that resulted in an error.
+
+### Reproducibility
+Include:
+- OS (WIN | MACOS | Linux)
+- DataJoint Element Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Expected Behavior
+A clear and concise description of what you expected to happen.
+
+### Screenshots
+If applicable, add screenshots to help explain your problem.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this report.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant
+  repositories.
+- Specific links to specific lines or a focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,5 @@
+blank_issues_enabled: false
+contact_links:
+  - name: DataJoint Contribution Guideline
+    url: https://docs.datajoint.org/python/community/02-Contribute.html
+    about: Please make sure to review the DataJoint Contribution Guidelines

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,57 @@
+---
+name: Feature request
+about: Suggest an idea for a new feature
+title: ''
+labels: 'enhancement'
+assignees: ''
+
+---
+
+## Feature Request
+
+### Problem
+
+A clear and concise description how this idea has manifested and the context. Elaborate
+on the need for this feature and/or what could be improved. Ex. I'm always frustrated
+when [...]
+
+### Requirements
+
+A clear and concise description of the requirements to satisfy the new feature. Detail
+what you expect from a successful implementation of the feature. Ex. When using this
+feature, it should [...]
+
+### Justification
+
+Provide the key benefits in making this a supported feature. Ex. Adding support for this
+feature would ensure [...]
+
+### Alternative Considerations
+
+Do you currently have a work-around for this? Provide any alternative solutions or
+features you've considered.
+
+### Related Errors
+Add any errors as a direct result of not exposing this feature.
+
+Please include steps to reproduce provided errors as follows:
+- OS (WIN | MACOS | Linux)
+- DataJoint Element Version
+- MySQL Version
+- MySQL Deployment Strategy (local-native | local-docker | remote)
+- Minimum number of steps to reliably reproduce the issue
+- Complete error stack as a result of evaluating the above steps
+
+### Screenshots
+If applicable, add screenshots to help explain your feature.
+
+### Additional Research and Context
+Add any additional research or context that was conducted in creating this feature request.
+
+For example:
+- Related GitHub issues and PR's either within this repository or in other relevant
+  repositories.
+- Specific links to specific lines or a focus within source code.
+- Relevant summary of Maintainers development meetings, milestones, projects, etc.
+- Any additional supplemental web references or links that would further justify this
+  feature request.

CHANGELOG.md

@@ -3,13 +3,17 @@
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
 ## [0.3.0] - 2022-10-7
+
 + Add - Function `prairieviewreader` to parse metadata from Bruker PrarieView acquisition system
 
+
 ## 0.2.1 - 2022-07-13
+
 + Add - Adopt `black` formatting
 + Add - Code of Conduct
 
 ## 0.2.0 - 2022-07-06
+
 + First release of `element-interface`.
 + Bugfix - Fix for `tifffile` import.
 + Add - Function `run_caiman` to trigger CNMF algorithm.
@@ -19,9 +23,11 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 + Update - Remove `extras_require` feature to allow this package to be published to PyPI.
 
 ## 0.1.0a1 - 2022-01-12
+
 + Change - Rename the package `element-data-loader` to `element-interface`.
 
 ## 0.1.0a0 - 2021-06-21
+
 + Add - Readers for: `ScanImage`, `Suite2p`, `CaImAn`.
 
 [0.3.0]: https://github.com/datajoint/element-interface/releases/tag/0.3.0

README.md

@@ -60,27 +60,24 @@ repositories for example usage of `element-interface`.
      loaded_dataset = suite2p_loader.Suite2p(output_dir)
      ```
 
-
 + Suite2p wrapper functions for triggering analysis
 
-     Each step of Suite2p (registration, segmentation and deconvolution) 
-     can be run independently for single plane tiff files. The functions in this
-     package will facilitate this process. Requirements include the [ops dictionary](
-     https://suite2p.readthedocs.io/en/latest/settings.html) and db dictionary.
-     These wrapper functions were developed primarily because `run_s2p` cannot 
-     individually run deconvolution using the `spikedetect` flag 
-     ([Suite2p Issue #718](https://github.com/MouseLand/suite2p/issues/718)).
+  + Functions to independently run Suite2p's motion correction, segmentation, and deconvolution steps. These functions currently work for single plane tiff files.  If running all Suite2p pre-processing steps concurrently, these functions are not required and one can run `suite2p.run_s2p()`.
 
-     ```python
-     from element_data_loader.suite2p_trigger import motion_correction_suite2p,
-     segmentation_suite2p, deconvolution_suite2p
-     from suite2p import default_ops
+  + These wrapper functions were developed primarily because `run_s2p` cannot individually run deconvolution using the `spikedetect` flag ([Suite2p Issue #718](https://github.com/MouseLand/suite2p/issues/718)).
 
-     ops = dict(default_ops(), nonrigid=False, two_step_registration=False)
-     ```
-     Details of db dictionary can be found [here](https://github.com/MouseLand/suite2p/blob/4b6c3a95b53e5581dbab1feb26d67878db866068/jupyter/run_pipeline_tiffs_or_batch.ipynb)
+  + Requirements
+    + [ops dictionary](https://suite2p.readthedocs.io/en/latest/settings.html)
+    + [db dictionary](https://github.com/MouseLand/suite2p/blob/4b6c3a95b53e5581dbab1feb26d67878db866068/jupyter/run_pipeline_tiffs_or_batch.ipynb)
+
+  + Note that the ops dictionary returned from the `motion_correction_suite2p` and `segmentation_suite2p` functions is only a subset of the keys generated with the `suite2p.default_ops()` function.
 
      ```python
+     import element_interface
+     import suite2p
+
+     ops = dict(suite2p.default_ops(), nonrigid=False, two_step_registration=False)
+
      db = {
           'h5py': [], # single h5 file path
           'h5py_key': 'data',
@@ -91,13 +88,13 @@ repositories for example usage of `element-interface`.
           }
 
      ops.update(do_registration=1, roidetect=False, spikedetect=False)
-     registration_ops = motion_registration_suite2p(ops, db)
+     motion_correction_ops = element_interface.suite2p_trigger.motion_correction_suite2p(ops, db)
 
-     registration_ops.update(do_registration=0, roidetect=True, spikedetect=False)
-     segmentation_ops = segmentation_suite2p(registration_ops, db)
+     motion_correction_ops.update(do_registration=0, roidetect=True, spikedetect=False)
+     segmentation_ops = element_interface.suite2p_trigger.segmentation_suite2p(motion_correction_ops, db)
 
      segmentation_ops.update(do_registration=0, roidetect=False, spikedetect=True)
-     spikes = deconvolution_suite2p(segmentation_ops, db)
+     spikes = element_interface.suite2p_trigger.deconvolution_suite2p(segmentation_ops, db)
      ```