New Tool: Extract frames with CV2

tools/extract_frames/.shed.yml

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+categories:
+  - Imaging
+description: Extract frames from .MP4 and .AVI
+long_description: This tools extract a user defined range of frames from an .MP4 or .AVI file and convert them to .TIFF files for further downstream analysis
+name: extract_frames 
+owner: ufz
+homepage_url: https://github.com/bmcv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/extract_frames

tools/extract_frames/creators.xml

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+../../macros/creators.xml

tools/extract_frames/cv2_extract_frames.py

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+import argparse
+import os
+from pathlib import Path
+from typing import Union
+
+import cv2
+
+
+def extract_frames(output_dir: Union[str, Path], video_path: Union[str, Path], start_time: int, end_time: int, convert_to_grey: str = "false") -> Path:
+    """
+    Extract frames from a video within a specified time range in seconds
+
+    Parameters
+    ----------
+        video_path: Path to the input video file
+
+        start_time: Start time in seconds
+
+        end_time: End time in seconds
+
+        output_dir: Directory where extracted frames will be saved
+
+        convert_to_gray: Whether to convert frames to grayscale
+
+    Returns:
+    ---------
+        Path to the directory containing the extracted frames.
+    """
+
+    try:
+        video = cv2.VideoCapture(video_path)
+
+        # get the video frames per second
+        fps = video.get(cv2.CAP_PROP_FPS)
+        print('Frames per second:', fps)
+        # get the video total frames
+        frame_count = video.get(cv2.CAP_PROP_FRAME_COUNT)
+        print('Total frames:', frame_count)
+
+        start_frame = int(start_time * fps)
+        end_frame = int(end_time * fps)
+        print(f'Starting extracting from frame {start_frame} until {end_frame}...')
+
+        video.set(cv2.CAP_PROP_POS_FRAMES, start_frame)
+        current_frame = start_frame
+
+        while current_frame <= end_frame:
+            ret, frame = video.read()
+            if not ret:
+                break
+
+            # Convert to single-channel grayscale
+            output_path = os.path.join(output_dir, f"frame_{current_frame:05d}.tiff")
+            if convert_to_grey == "true":
+                cv2.imwrite(output_path, cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY), [cv2.IMWRITE_TIFF_COMPRESSION, 1])
+            else:
+                cv2.imwrite(output_path, frame, [cv2.IMWRITE_TIFF_COMPRESSION, 1])
+            current_frame += 1
+
+        video.release()
+
+        print('Extraction was successfully executed. Enjoy your frames.')
+
+    except IOError:
+        print("Cannot open video file")
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Extract frames from video files")
+    parser.add_argument('output_dir', help="Name of the output folder")
+    parser.add_argument('-v', '--video_path', required=True, help="Path to the video to convert")
+    parser.add_argument('-s', '--start_time', required=True, type=float, help="Start time in seconds")
+    parser.add_argument('-e', '--end_time', required=True, type=float, help="End time in seconds")
+    parser.add_argument('-c', '--convert_to_grey', required=False, type=str, help="Convert the file to grayscale")
+
+    args = parser.parse_args()
+
+    extract_frames(args.output_dir, video_path=args.video_path, start_time=args.start_time, end_time=args.end_time, convert_to_grey=args.convert_to_grey)

tools/extract_frames/cv2_extract_frames.xml

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+<tool id="extract_frames" name="Extract video frames" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>with cv2</description>
+    <macros>
+        <token name="@TOOL_VERSION@">0.1</token>
+        <token name="@VERSION_SUFFIX@">1</token>
+        <import>tests.xml</import>
+        <import>creators.xml</import>
+    </macros>
+    <creator>
+        <expand macro="creators/rmassei"/>
+    </creator>
+    <requirements>
+        <requirement type="package" version="4.13.0">opencv</requirement>
+    </requirements>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        mkdir ./output_frames &&
+
+        python "$__tool_directory__/cv2_extract_frames.py" output_frames
+        -v $video_path 
+        -s $start_time 
+        -e $end_time 
+        -c $convert_to_grey
+
+        && ls -l ./output_frames
+        ]]>
+    </command>
+    <inputs>
+        <param argument="video_path" type="data" optional="False" format="mp4,avi" label="Input video to convert" help="Path to the video to convert"/>
+        <param argument="start_time" type="float" optional="False" label="Start time (seconds)" help="Start time in seconds"/>
+        <param argument="end_time" type="float" optional="False" label="End time (seconds)" help="End time in seconds"/>
+        <param argument="convert_to_grey" type="boolean" label="Convert output to grayscale?" help="Convert the file to grayscale"/>
+    </inputs>
+     <outputs>
+        <collection name="frames" type="list" label="Output frames">
+            <discover_datasets directory="output_frames" format="tiff" pattern="__name__"/>
+        </collection>
+    </outputs>
+        <tests>
+        <test>
+            <!-- test MP4 w/o grayscale conversion -->
+            <param name="video_path" value="input1.mp4"/>
+            <param name="start_time" value="0"/>
+            <param name="end_time" value="1"/>
+            <param name="convert_to_grey" value="False"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_00001.tiff" value="frame_00001.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_00002.tiff" value="frame_00002.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <!-- test MP4 w grayscale conversion -->
+            <param name="video_path" value="input1.mp4"/>
+            <param name="start_time" value="0"/>
+            <param name="end_time" value="1"/>
+            <param name="convert_to_grey" value="True"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_00003.tiff" value="frame_00003.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_00004.tiff" value="frame_00004.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <!-- test AVI w/o grayscale conversion -->
+            <param name="video_path" value="input2.avi"/>
+            <param name="start_time" value="0"/>
+            <param name="end_time" value="1"/>
+            <param name="convert_to_grey" value="False"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_00005.tiff" value="frame_00005.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_00006.tiff" value="frame_00006.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <!-- test AVI w grayscale conversion -->
+            <param name="video_path" value="input2.avi"/>
+            <param name="start_time" value="0"/>
+            <param name="end_time" value="1"/>
+            <param name="convert_to_grey" value="True"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_00007.tiff" value="frame_00007.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_00008.tiff" value="frame_00008.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+
+        **Extract single frames as TIFFs from MP4 and AVI files**
+
+        Frames captured within a specified time interval (in seconds) will be extracted from the video file as individual TIFF images. 
+        Optionally, the extracted frames can be converted to grayscale. 
+
+        **Codecs Support:** The library OpenCV's cv2 supports various video codecs including MPEG1, MPEG2, MPEG4, H264, HEVC, VP8, VP9, and more. Check
+        the documentation for more information on the supported codecs.
+
+    </help>
+    <citations>
+            <citation type="bibtex">@article{opencv_library,
+            author = {Bradski, G.},
+            citeulike-article-id = {2236121},
+            journal = {Dr. Dobb's Journal of Software Tools},
+            keywords = {bibtex-import},
+            posted-at = {2008-01-15 19:21:54},
+            priority = {4},
+            title = {{The OpenCV Library}},
+            year = {2000}
+            }</citation>
+    </citations>
+</tool>
+

tools/extract_frames/tests.xml

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+../../macros/tests.xml