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New Tool: Extract frames with CV2 (#207)
* added new tools to extract frames in cv2 * linted the python script * corrected import order in the python script * fix: reduce video resolution to have smaller files * Apply suggestions from code review Co-authored-by: Leonid Kostrykin <void@evoid.de> * fix: change argument to name in the XML inputs * feature: renamed the folder and convert the tool into a suite * fix: Revise codec support details in cv2_extract_frames.xml Updated codec support information and added feedback request. * refactor: removed old structure * fix: corrected the linting error, sheed and xml * fix: small review fixes, help section plus formatting Co-authored-by: Leonid Kostrykin <void@evoid.de> * fix: standardize the sheed structure * fix: add default value to the input parameters * minor code fixes for better input and error handling Co-authored-by: Leonid Kostrykin <void@evoid.de> * Make `end_time` optional * Add min attribute to start_time parameter * Fix XML formatting for start_time parameter * fix: fixed the format code 'd' error * feature: new test for endtime equal 0 AND negative * fix: Update XML to use single quotes for command arguments * Fix quotes in cv2_extract_frames.xml command --------- Co-authored-by: Leonid Kostrykin <void@evoid.de>
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‎tools/cv2/.shed.yml‎

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owner: imgteam
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suite:
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name: suite_cv2
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description: Suite of tools for wrapping the cv2 python module
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long_description: |
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OpenCV is a library of programming functions mainly for real-time computer vision. OpenCV is the world's biggest and open source vision library
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with more the 2500 algorithms for tasks such as object detection, facial recognition, and image stitching,
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The Python interface cv2 allows accessing the functionalities provided by the OpenCV library.
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This tool suite provides wrappers for the cv2 Python package enabling processing of image and video in Galaxy using OpenCV.
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auto_tool_repositories:
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name_template: "{{ tool_id }}"
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description_template: "{{ tool_name }}"
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long_description: |
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Enables processing image and video in Galaxy using OpenCV. Based on the cv2 Python package.
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type: unrestricted
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categories:
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- Imaging
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homepage_url: https://github.com/opencv/opencv
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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
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import os
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from pathlib import Path
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from typing import Optional, Union
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import cv2
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def _normalize_frame_number(
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frame_count: int,
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frame: int,
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) -> int:
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"""
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Translate negative frame numbers into positives by counting from the end.
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Raises:
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-------
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ValueError: The given frame is beyond the end of the sequence.
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Returns:
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--------
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Integer number between 0 and num_frames - 1.
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"""
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if frame >= frame_count:
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raise ValueError(
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f"Frame {frame} is beyond the end of the sequence ({frame_count} frames).",
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)
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return frame % frame_count
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def extract_frames(
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output_dir: Union[str, Path],
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video_path: Union[str, Path],
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start_time: float,
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end_time: Optional[float],
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convert_to_grey: str = "false",
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) -> Path:
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"""
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Extract frames from a video within a specified time range in seconds
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Parameters
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----------
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video_path: Path to the input video file
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start_time: Start time in seconds
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end_time: End time in seconds
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output_dir: Directory where extracted frames will be saved
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convert_to_gray: Whether to convert frames to grayscale
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Returns:
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---------
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Path to the directory containing the extracted frames.
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"""
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try:
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video = cv2.VideoCapture(video_path)
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# get the video frames per second
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fps = video.get(cv2.CAP_PROP_FPS)
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print('Frames per second:', fps)
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# get the video total frames
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frame_count = video.get(cv2.CAP_PROP_FRAME_COUNT)
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print('Total frames:', frame_count)
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# determine first and last frame of the sequence to extract
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start_frame = _normalize_frame_number(
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frame_count,
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round(start_time * fps),
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)
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end_frame = (
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_normalize_frame_number(
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frame_count,
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round(end_time * fps),
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)
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if end_time is not None
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else frame_count - 1
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)
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if start_frame > end_frame:
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raise ValueError(
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f"Start frame {start_frame} is beyond the end frame {end_frame}.",
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)
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else:
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print(
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f'Starting extracting from frame {start_frame} until {end_frame}...',
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)
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video.set(cv2.CAP_PROP_POS_FRAMES, start_frame)
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current_frame = start_frame
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while current_frame <= end_frame:
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ret, frame = video.read()
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if not ret:
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break
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# Convert to single-channel grayscale
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output_path = os.path.join(output_dir, f"frame_{int(current_frame):d}.tiff")
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if convert_to_grey == "true":
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cv2.imwrite(output_path, cv2.cvtColor(frame, cv2.COLOR_BGR2GRAY), [cv2.IMWRITE_TIFF_COMPRESSION, 1])
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else:
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cv2.imwrite(output_path, frame, [cv2.IMWRITE_TIFF_COMPRESSION, 1])
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current_frame += 1
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video.release()
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print('Extraction was successfully executed. Enjoy your frames.')
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except IOError:
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exit("Cannot open video file.")
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except ValueError as err:
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exit(err.args[0])
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if __name__ == "__main__":
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parser = argparse.ArgumentParser(description="Extract frames from video files")
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parser.add_argument('output_dir', help="Name of the output folder")
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parser.add_argument('-v', '--video_path', required=True, help="Path to the video to convert")
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parser.add_argument('-s', '--start_time', required=True, type=float, help="Start time in seconds")
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parser.add_argument('-e', '--end_time', type=float, help="End time in seconds")
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parser.add_argument('-c', '--convert_to_grey', required=False, type=str, help="Convert the file to grayscale")
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args = parser.parse_args()
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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">
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<description>with cv2</description>
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<macros>
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<token name="@TOOL_VERSION@">4.13.0</token>
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<token name="@VERSION_SUFFIX@">0</token>
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<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>
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<import>tests.xml</import>
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<import>creators.xml</import>
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</macros>
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<creator>
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<expand macro="creators/rmassei"/>
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</creator>
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<edam_operations>
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<edam_operation>operation_3443</edam_operation>
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</edam_operations>
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<xrefs>
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<xref type="biii">opencv</xref>
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</xrefs>
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<requirements>
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<requirement type="package" version="4.13.0">opencv</requirement>
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</requirements>
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<required_files>
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<include type="literal" path="cv2_extract_frames.py"/>
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</required_files>
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<command detect_errors="aggressive">
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<![CDATA[
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mkdir ./output_frames &&
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python '$__tool_directory__/cv2_extract_frames.py' output_frames
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-v '$video_path'
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-s '$start_time'
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#if str($end_time) != ""
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-e '$end_time'
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#end if
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-c '$convert_to_grey'
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&& ls -l ./output_frames
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]]>
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</command>
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<inputs>
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<param name="video_path" type="data" optional="False" format="mp4,avi" label="Input video to convert"/>
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<param name="start_time" type="float" value="0" optional="false" label="Start time"
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help="Start time in seconds. @HELP_SECONDS@"/>
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<param name="end_time" type="float" optional="true" label="End time"
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help="End time in seconds (optional). Leave empty to extract the sequence until the end of the video. @HELP_SECONDS@"/>
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<param name="convert_to_grey" type="boolean" label="Convert output to single-channel grayscale?"
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help="Convert the file to grayscale (will be RGB otherwise)."/>
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</inputs>
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<outputs>
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<collection name="frames" type="list" label="Output frames">
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<discover_datasets directory="output_frames" format="tiff" pattern="__name__"/>
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</collection>
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</outputs>
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<tests>
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<test>
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<!-- test MP4 w/o grayscale conversion -->
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<param name="video_path" value="input1.mp4"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="0.1"/>
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<param name="convert_to_grey" value="False"/>
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<output_collection name="frames" type="list">
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<expand macro="tests/intensity_image_diff/element" name="frame_0.tiff" value="frame_0.tiff" ftype="tiff"/>
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<expand macro="tests/intensity_image_diff/element" name="frame_1.tiff" value="frame_1.tiff" ftype="tiff"/>
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</output_collection>
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</test>
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<test>
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<!-- test MP4 w grayscale conversion -->
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<param name="video_path" value="input1.mp4"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="0.1"/>
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<param name="convert_to_grey" value="True"/>
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<output_collection name="frames" type="list">
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<expand macro="tests/intensity_image_diff/element" name="frame_2.tiff" value="frame_2.tiff" ftype="tiff"/>
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<expand macro="tests/intensity_image_diff/element" name="frame_3.tiff" value="frame_3.tiff" ftype="tiff"/>
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</output_collection>
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</test>
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<test>
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<!-- test AVI w/o grayscale conversion -->
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<param name="video_path" value="input2.avi"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="1"/>
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<param name="convert_to_grey" value="False"/>
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<output_collection name="frames" type="list">
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<expand macro="tests/intensity_image_diff/element" name="frame_4.tiff" value="frame_4.tiff" ftype="tiff"/>
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<expand macro="tests/intensity_image_diff/element" name="frame_5.tiff" value="frame_5.tiff" ftype="tiff"/>
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</output_collection>
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</test>
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<test>
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<!-- test AVI w grayscale conversion -->
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<param name="video_path" value="input2.avi"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="1"/>
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<param name="convert_to_grey" value="True"/>
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<output_collection name="frames" type="list">
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<expand macro="tests/intensity_image_diff/element" name="frame_6.tiff" value="frame_6.tiff" ftype="tiff"/>
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<expand macro="tests/intensity_image_diff/element" name="frame_7.tiff" value="frame_7.tiff" ftype="tiff"/>
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</output_collection>
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</test>
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<test>
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<!-- test AVI with endtime 0 -->
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<param name="video_path" value="input2.avi"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="0"/>
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<param name="convert_to_grey" value="True"/>
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<output_collection name="frames" type="list" count="1"/>
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</test>
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<test>
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<!-- test MP4 with endtime negative-->
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<param name="video_path" value="input1.mp4"/>
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<param name="start_time" value="0"/>
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<param name="end_time" value="-1"/>
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<param name="convert_to_grey" value="True"/>
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<output_collection name="frames" type="list" count="238"/>
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</test>
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</tests>
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<help>
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**Extract a sequence of image frames as TIFFs from MP4 and AVI files.**
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Frames captured within a specified time interval (in seconds) will be extracted from the video file as individual TIFF images.
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Optionally, the extracted frames can be converted to grayscale.
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**Codecs Support:**
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The tool was tested with H.264 and H.265 (HEVC) video codecs.
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The tool may support other codecs, though this has not been tested yet.
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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.
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</help>
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<citations>
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<citation type="bibtex">@article{opencv_library,
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author = {Bradski, G.},
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citeulike-article-id = {2236121},
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journal = {Dr. Dobb's Journal of Software Tools},
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keywords = {bibtex-import},
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posted-at = {2008-01-15 19:21:54},
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priority = {4},
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title = {{The OpenCV Library}},
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year = {2000}
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}</citation>
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</citations>
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</tool>
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‎tools/cv2/test-data/frame_0.tiff‎

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‎tools/cv2/test-data/frame_1.tiff‎

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‎tools/cv2/test-data/frame_2.tiff‎

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‎tools/cv2/test-data/frame_3.tiff‎

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‎tools/cv2/test-data/frame_4.tiff‎

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‎tools/cv2/test-data/frame_5.tiff‎

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