fix: incorrect if statement for manual depth range

fix: incorrect if statement for manual depth range

.github/pull_request_template.md

@@ -0,0 +1,29 @@
+<!--- Provide a general summary of your changes in the Title above -->
+<!--- Pull request titles must use the [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/#summary) format -->
+
+## Issue being fixed or feature implemented
+<!--- Why is this change required? What problem does it solve? -->
+<!--- If it fixes an open issue, please link to the issue here. -->
+
+
+## What was done?
+<!--- Describe your changes in detail -->
+
+
+## How Has This Been Tested?
+<!--- Please describe in detail how you tested your changes. -->
+<!--- Include details of your testing environment, and the tests you ran to -->
+<!--- see how your change affects other areas of the code, etc. -->
+
+
+## Breaking Changes
+<!--- Please describe any breaking changes your code introduces and verify that -->
+<!--- the title includes "!" following the conventional commit type (e.g. "feat!: ..."-->
+
+
+## Checklist:
+<!--- Go over all the following points, and put an `x` in all the boxes that apply. -->
+- [ ] I have performed a self-review of my own code
+- [ ] I have commented my code, particularly in hard-to-understand areas
+- [ ] I have added or updated relevant unit/integration/functional/e2e tests
+- [ ] I have made corresponding changes to the documentation

README.md

@@ -4,15 +4,10 @@
 
 [![codecov](https://codecov.io/gh/dattalab/moseq2-extract/branch/test-suite/graph/badge.svg?token=ICPjpMMwYZ)](https://codecov.io/gh/dattalab/moseq2-extract)
 
-Welcome to moseq2, the latest version of a software package for mouse tracking in depth videos first developed by Alex Wiltschko in the Datta Lab at Harvard Medical School.
+# [Documentation: MoSeq2 Wiki](https://github.com/dattalab/moseq2-app/wiki)
+You can find more information about MoSeq Pipeline, installation, step-by-step instructions, documentation for Command Line Interface(CLI), tutorials etc in [MoSeq2 Wiki](https://github.com/dattalab/moseq2-app/wiki).
 
-Latest version is `0.7.0`
-
-***
-
-## Features
-Below are the commands/functionality that moseq2-extract currently affords. 
-They are accessible via CLI or Jupyter Notebook in [moseq2-app](https://github.com/dattalab/moseq2-app/tree/release).
+You can run `moseq2-extract --version` to check the current version and `moseq2-extract --help` to see all the commands.
 ```bash
 Usage: moseq2-extract [OPTIONS] COMMAND [ARGS]...
 
@@ -33,69 +28,10 @@ Commands:
   generate-index      Generates an index YAML file containing all extracted...
 ```
 
-### CLI Exclusive Functions
-```bash
-batch-extract       Batch processes all the raw depth recordings located...
-convert-raw-to-avi  Converts/Compresses a raw depth file into an avi file...
-copy-slice          Copies a segment of an input depth recording into a...
-```
-
-### GUI Exclusive Function
-```bash
-extract_found_sessions() Extracts all found data within a given input_dir, 
- AND searches for individual session configuration parameters in the session_config.yaml
-```
-
-Run any command with the `--help` flag to display all available options and their descriptions.
-
-***
-
-## Documentation
-
-MoSeq2 uses `sphinx` to generate the documentation in HTML and PDF forms. To install `sphinx`, follow the commands below:
-```.bash
-pip install sphinx==3.0.3 sphinx_click==2.5.0
-pip install sphinx-rtd-theme
-pip install rst2pdf
-``` 
-
-All documentation regarding moseq2-extract can be found in the `Documentation.pdf` file in the root directory,
-an HTML ReadTheDocs page can be generated via running the `make html` in the `docs/` directory.
-
-To generate a PDF version of the documentation, simply run `make pdf` in the `docs/` directory.
-
-For information on getting started, check out the [MoSeq Roadmap](https://github.com/dattalab/moseq2-docs/wiki).
-***
-
-## Examples
-
-### Example `find-roi` Outputs
-
-#### Round Arena ROI and Background
-
-![alt text](media/plt_example.png)<br><br>
-
-#### Y-Maze Arena (from Kinect v2 Camera)
-
-![alt text ](media/found_arena.png)
-
-#### Convex-shaped Bucket (\\_/) (from Azure Camera)
-Dilated Background and ROI respectively.
-
-![alt text](media/bg_roi_dilated.png)
-![alt text](media/roi_dilated.png)
-
-#### Rectangular Arena (from RealSense)
-ROI and Weighted Background Image respectively.
-
-![alt text](media/rs_roi_example.png)
-
-### Example Extraction
-
-![alt text](media/good_recording.gif)
-
-***
-
-## Contributing
 
-If you would like to contribute, fork the repository and issue a pull request.  
+# Community Support and Contributing
+- Please join [![MoSeq Slack Channel](https://img.shields.io/badge/slack-MoSeq-blue.svg?logo=slack)](https://moseqworkspace.slack.com) to post questions and interactive with MoSeq developers and users.
+- If you encounter bugs, errors or issues, please submit a Bug report [here](https://github.com/dattalab/moseq2-app/issues/new/choose). We encourage you to check out the [troubleshooting and tips section](https://github.com/dattalab/moseq2-app/wiki/Troubleshooting-and-Tips) and search your issues in [the existing issues](https://github.com/dattalab/moseq2-app/issues) first.   
+- If you want to see certain features in MoSeq or you have new ideas, please submit a Feature request [here](https://github.com/dattalab/moseq2-app/issues/new/choose).
+- If you want to contribute to our codebases, please check out our [Developer Guidelines](https://github.com/dattalab/moseq2-app/wiki/MoSeq-Developer-Guidelines).
+- Please tell us what you think by filling out [this user survey](https://forms.gle/FbtEN8E382y8jF3p6).

moseq2_extract/__init__.py

@@ -1 +1 @@
-__version__ = "0.8.1"
+__version__ = "v1.0.1beta"

moseq2_extract/helpers/wrappers.py

@@ -189,7 +189,7 @@ def get_roi_wrapper(input_file, config_data, output_dir=None):
     write_image(join(output_dir, 'bground.tiff'), bground_im, scale=True)
 
     # readjust depth range
-    if config_data.get('manual_set_depth_range', False):
+    if not config_data.get('manual_set_depth_range', False):
         # search for depth values between the max distance and the halfway point to the camera
         print('Automatically setting depth range. To manually set range values,'
               ' set "manual_set_depth_range" to True.\n For CLI users: use the --manual-set-depth-range flag.')