Other formats¶
PIMS¶
Through PIMS, MorphoCut supports reading Bioformats and Video.
“PIMS is a lazy-loading interface to sequential data with numpy-like slicing.”
Note
PIMS is required to use the nodes defined in this module.
-
morphocut.pims.
BioformatsReader
(path, meta, series=None, **kwargs)[source]¶ Stream Read frames from Bio-Formats files.
Bio-Formats is a software tool for reading and writing image data using standardized, open formats. It is able to read over 150 file formats, including OME-TIFF and Amnis FlowSight (.cif).
Note
JPype is required to use this reader.
On first use of BioformatsReader, the required java library loci_tools.jar will be automatically downloaded from openmicroscopy.org.
- Parameters
path (str) – Path to a Bioformats file.
meta (bool, optional) – When true, the metadata object is generated. Takes time to build.
series (int, optional) – Active image series index. Defaults to None, meaning that all series are read.
**kwargs – Additional keyword parameters for pims.BioformatsReader
Example
frame, series = BioformatsReader(path) # frame (pims.Frame): The frame. # frame.frame_no (int): Frame number. # frame.metadata (dict): Frame metadata. # series (int): The series extracted from the file.
-
morphocut.pims.
VideoReader
(path, **kwargs)[source]¶ Stream Read frames from video files.
Note
PyAV is required to use this reader.
- Parameters
path – Path to a video file.
**kwargs – Additional keyword parameters for
pims.PyAVReaderIndexed
.
Example
frame = VideoReader(path) # frame (pims.Frame): The frame. # frame.frame_no (int): Frame number. # frame.metadata (dict): Frame metadata.
Example¶
from morphocut import Pipeline
from morphocut.image import ImageWriter
from morphocut.pims import VideoReader
from morphocut.str import Format
with Pipeline() as p:
frame = VideoReader("/path/to/video.avi")
filename = Format("/output/path/frame_#{}.png", frame.frame_no)
ImageWriter(filename, frame)
p.run()
Contributed¶
Stream Read an archive of images and metadata that is importable to EcoTaxa. |
|
Create an archive of images and metadata that is importable to EcoTaxa. |