New Tool: Extract frames with CV2

tools/cv2/.shed.yml

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+owner: imgteam
+
+suite:
+  name: suite_cv2
+
+  description: Suite of tools for wrapping the cv2 python module
+
+  long_description: |
+    OpenCV is a library of programming functions mainly for real-time computer vision. OpenCV is the world's biggest and open source vision library
+    with more the 2500 algorithms for tasks such as object detection, facial recognition, and image stitching, 
+    The Python interface cv2 allows accessing the functionalities provided by the OpenCV library.
+
+    This tool suite provides wrappers for the cv2 Python package enabling processing of image and video in Galaxy using OpenCV.
+
+
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "{{ tool_name }}"
+
+long_description: |
+  Enables processing image and video in Galaxy using OpenCV. Based on the cv2 Python package.
+
+type: unrestricted
+
+categories:
+  - Imaging
+
+homepage_url: https://github.com/opencv/opencv
+remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tools/cv2

tools/cv2/creators.xml

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

tools/cv2/cv2_extract_frames.py

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+import argparse
+import os
+from pathlib import Path
+from typing import Optional, Union
+
+import cv2
+
+
+def _normalize_frame_number(
+    frame_count: int,
+    frame: int,
+) -> int:
+    """
+    Translate negative frame numbers into positives by counting from the end.
+
+    Raises:
+    -------
+        ValueError: The given frame is beyond the end of the sequence.
+
+    Returns:
+    --------
+        Integer number between 0 and num_frames - 1.
+    """
+    if frame >= frame_count:
+        raise ValueError(
+            f"Frame {frame} is beyond the end of the sequence ({frame_count} frames).",
+        )
+    return frame % frame_count
+
+
+def extract_frames(
+    output_dir: Union[str, Path],
+    video_path: Union[str, Path],
+    start_time: float,
+    end_time: Optional[float],
+    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)
+
+        # determine first and last frame of the sequence to extract
+        start_frame = _normalize_frame_number(
+            frame_count,
+            round(start_time * fps),
+        )
+        end_frame = (
+            _normalize_frame_number(
+                frame_count,
+                round(end_time * fps),
+            )
+            if end_time is not None
+            else frame_count - 1
+        )
+        if start_frame > end_frame:
+            raise ValueError(
+                f"Start frame {start_frame} is beyond the end frame {end_frame}.",
+            )
+        else:
+            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_{int(current_frame):d}.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:
+        exit("Cannot open video file.")
+
+    except ValueError as err:
+        exit(err.args[0])
+
+
+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', 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/cv2/cv2_extract_frames.xml

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+<tool id="cv2_extract_frames" name="Extract video frames" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
+    <description>with cv2</description>
+    <macros>
+        <token name="@TOOL_VERSION@">4.13.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@HELP_SECONDS@">Use a negative value to specify the time from the end of the video (e.g., a value of -1 corresponds to "1 second before the end of the video").</token>
+        <import>tests.xml</import>
+        <import>creators.xml</import>
+    </macros>
+    <creator>
+        <expand macro="creators/rmassei"/>
+    </creator>
+    <edam_operations>
+        <edam_operation>operation_3443</edam_operation>
+    </edam_operations>
+    <xrefs>
+        <xref type="biii">opencv</xref>
+    </xrefs>
+    <requirements>
+        <requirement type="package" version="4.13.0">opencv</requirement>
+    </requirements>
+    <required_files>
+        <include type="literal" path="cv2_extract_frames.py"/>
+    </required_files>
+    <command detect_errors="aggressive">
+        <![CDATA[
+        mkdir ./output_frames &&
+
+        python '$__tool_directory__/cv2_extract_frames.py' output_frames
+        -v '$video_path' 
+        -s '$start_time' 
+        #if str($end_time) != ""
+            -e '$end_time' 
+        #end if
+        -c '$convert_to_grey'
+
+        && ls -l ./output_frames
+        ]]>
+    </command>
+    <inputs>
+        <param name="video_path" type="data" optional="False" format="mp4,avi" label="Input video to convert"/>
+        <param name="start_time" type="float" value="0" optional="false" label="Start time"
+               help="Start time in seconds. @HELP_SECONDS@"/>
+        <param name="end_time" type="float" optional="true" label="End time"
+               help="End time in seconds (optional). Leave empty to extract the sequence until the end of the video. @HELP_SECONDS@"/>
+        <param name="convert_to_grey" type="boolean" label="Convert output to single-channel grayscale?"
+               help="Convert the file to grayscale (will be RGB otherwise)."/>
+    </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="0.1"/>
+            <param name="convert_to_grey" value="False"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_0.tiff" value="frame_0.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_1.tiff" value="frame_1.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="0.1"/>
+            <param name="convert_to_grey" value="True"/>
+            <output_collection name="frames" type="list">
+                <expand macro="tests/intensity_image_diff/element" name="frame_2.tiff" value="frame_2.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_3.tiff" value="frame_3.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_4.tiff" value="frame_4.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_5.tiff" value="frame_5.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_6.tiff" value="frame_6.tiff" ftype="tiff"/>
+                <expand macro="tests/intensity_image_diff/element" name="frame_7.tiff" value="frame_7.tiff" ftype="tiff"/>
+            </output_collection>
+        </test>
+        <test>
+            <!-- test AVI with endtime 0 -->
+            <param name="video_path" value="input2.avi"/>
+            <param name="start_time" value="0"/>
+            <param name="end_time" value="0"/>
+            <param name="convert_to_grey" value="True"/>
+            <output_collection name="frames" type="list" count="1"/>
+        </test>
+        <test>
+            <!-- test MP4 with endtime negative-->
+            <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" count="238"/>
+        </test>
+    </tests>
+    <help>
+
+        **Extract a sequence of image 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 tool was tested with H.264 and H.265 (HEVC) video codecs.
+        The tool may support other codecs, though this has not been tested yet. 
+        If you have successfully converted files using alternative video formats or codecs, we would be grateful for your feedback at https://github.com/BMCV/galaxy-image-analysis.
+
+    </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/cv2/tests.xml

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