![]() ![]() Karhohs, Investigation, Methodology, Software, # 1 Minh Doan, Methodology, Software, Writing – original draft, Writing – review & editing, 1 Liya Ding, Data curation, Methodology, Software, Validation, Writing – review & editing, 4 Susanne M. Cimini, Conceptualization, Investigation, Methodology, Project administration, Software, Validation, Writing – review & editing, # 1 Kyle W. # The workspace object has access to the measurements # and the image set/image set list which can be used # to use/view/store/whatever output data.Claire McQuin, Conceptualization, Formal analysis, Software, Writing – original draft, Writing – review & editing, # 1 Allen Goodman, Conceptualization, Investigation, Software, # 1 Vasiliy Chernyshev, Data curation, Investigation, Methodology, Software, Validation, Visualization, Writing – review & editing, # 2, 3 Lee Kamentsky, Conceptualization, Software, # 1 Beth A. # Yes, we really do have to create a new workspace for each module # because the module attribute is required. group_number = 1 # Run the modules! workspace = None for module in pipeline. # We can only run one group - set the group index to 1. # Persist the object set here (for now, see workspace TODO) object_set = cellprofiler. # Create the image set, and add the image data image_set_list = cellprofiler. # Create and load the pipeline pipeline = cellprofiler. :param output_dir: (str) name of directory to store result in /data :param output_prefix: (str) the prefix of the output csv files :return """ # Run without the gui. ccpipe file (e.g.,test.cppipe) :param file_list: (list) list of absolute file paths. """Apply a CellProfiler pipeline file to a set of images. # Code adapted from def run_pipeline( pipeline_name, file_list, output_dir, output_prefix): Pipeline_filename = root+"ExampleFly.cppipe" # This should match what NamesAndTypes would produce. Root = "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/CellProfiler/cellprofiler/data/examples/ExampleFly/" # to use/view/store/whatever output data. # and the image set/image set list which can be used # The workspace object has access to the measurements # because the module attribute is required. # Yes, we really do have to create a new workspace for each module # Persist the object set here (for now, see workspace TODO) Image_set.add(image_name, (input_pixels)) Image_set = image_set_list.get_image_set(0)įor image_name, input_pixels in image_eritems(): # Create the image set, and add the image data (os.path.abspath('./CellProfiler/cellprofiler/utilities'))ĭef run_pipeline(pipeline_filename, image_dict): (os.path.abspath('./CellProfiler/cellprofiler')) Print ("exists: " if os.path.isfile(path) else "missing: ") + path Javabridge.class_for_name("")Ĭlasspath = javabridge.JClassWrapper('').getProperty('') Javabridge.start_vm(class_path=bioformats.JARS+) Result = self]įile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\utilities\hdf5_dict.py", line 379, in _getitem_Īssert feature_exists, "Feature does not exist".format(feature_name, object_name)ĪssertionError: Feature ImageSet_ImageSet for Image does not exist Vals = self.hdf5_dictįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\utilities\hdf5_dict.py", line 374, in _getitem_ Workspace = run_pipeline(pipeline_filename, images)įile "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/Testing.py", line 75, in run_pipelineįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\modules\namesandtypes.py", line 1731, in runįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\modules\**namesandtypes.py**", line 1663, in get_imagesetīlob = mįile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\measurement.py", line 368, in _getitem_įile "C:\Users\mayda\PycharmProjects\notebooks\Bio\CellProfiler\CellProfiler\cellprofiler\measurement.py", line 963, in get_measurement File "C:/Users/mayda/PycharmProjects/notebooks/Bio/CellProfiler/Testing.py", line 94, in ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |