How to use the cellprofiler.image.ImageSetList function in CellProfiler

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github CellProfiler / CellProfiler / tests / modules / test_identifyobjectsingrid.py View on Github external
def make_workspace(gridding, labels=None):
    module = cellprofiler.modules.identifyobjectsingrid.IdentifyObjectsInGrid()
    module.set_module_num(1)
    module.grid_name.value = GRID_NAME
    module.output_objects_name.value = OUTPUT_OBJECTS_NAME
    module.guiding_object_name.value = GUIDING_OBJECTS_NAME
    image_set_list = cellprofiler.image.ImageSetList()
    object_set = cellprofiler.object.ObjectSet()
    if labels is not None:
        my_objects = cellprofiler.object.Objects()
        my_objects.segmented = labels
        object_set.add_objects(my_objects, GUIDING_OBJECTS_NAME)
    pipeline = cellprofiler.pipeline.Pipeline()

    def callback(caller, event):
        assert not isinstance(event, cellprofiler.pipeline.RunExceptionEvent)

    pipeline.add_listener(callback)
    pipeline.add_module(module)
    workspace = cellprofiler.workspace.Workspace(
        pipeline,
        module,
        image_set_list.get_image_set(0),
github CellProfiler / CellProfiler / tests / modules / test_tile.py View on Github external
def make_place_workspace(images):
    image_set_list = cellprofiler.image.ImageSetList()
    image_set = image_set_list.get_image_set(0)
    module = cellprofiler.modules.tile.Tile()
    module.set_module_num(1)
    module.tile_method.value = cellprofiler.modules.tile.T_WITHIN_CYCLES
    module.output_image.value = OUTPUT_IMAGE_NAME
    module.wants_automatic_rows.value = False
    module.wants_automatic_columns.value = True
    module.rows.value = 1
    for i, image in enumerate(images):
        image_name = input_image_name(i)
        if i == 0:
            module.input_image.value = image_name
        else:
            if len(module.additional_images) <= i:
                module.add_image()
            module.additional_images[i - 1].input_image_name.value = image_name
github CellProfiler / CellProfiler / tests / modules / test_calculatestatistics.py View on Github external
for feature in list(odict.keys()):
            m.add_all_measurements(object_name, feature, odict[feature])
            if nimages is None:
                nimages = len(odict[feature])
            else:
                assert nimages == len(odict[feature])
            if (
                object_name == cellprofiler.measurement.IMAGE
                and feature in dose_measurements
            ):
                if len(module.dose_values) > 1:
                    module.add_dose_value()
                dv = module.dose_values[-1]
                dv.measurement.value = feature
    m.image_set_number = nimages
    image_set_list = cellprofiler.image.ImageSetList()
    for i in range(nimages):
        image_set = image_set_list.get_image_set(i)
    workspace = cellprofiler.workspace.Workspace(
        pipeline, module, image_set, cellprofiler.object.ObjectSet(), m, image_set_list
    )
    return workspace, module
github CellProfiler / CellProfiler / tests / modules / test_measureobjectoverlap.py View on Github external
j - j component of pixel coordinates
    l - label """

    module = cellprofiler.modules.measureobjectoverlap.MeasureObjectOverlap()
    module.set_module_num(1)
    module.object_name_GT.value = GROUND_TRUTH_OBJ
    module.object_name_ID.value = ID_OBJ
    module.wants_emd.value = True
    pipeline = cellprofiler.pipeline.Pipeline()

    def callback(caller, event):
        assert not isinstance(event, cellprofiler.pipeline.RunExceptionEvent)

    pipeline.add_listener(callback)
    pipeline.add_module(module)
    image_set_list = cellprofiler.image.ImageSetList()
    image_set = image_set_list.get_image_set(0)

    for name, d in (
        (GROUND_TRUTH_OBJ_IMAGE_NAME, ground_truth),
        (ID_OBJ_IMAGE_NAME, id),
    ):
        image = cellprofiler.image.Image(
            d["image"], mask=d.get("mask"), crop_mask=d.get("crop_mask")
        )
        image_set.add(name, image)
    object_set = cellprofiler.object.ObjectSet()
    for name, d in ((GROUND_TRUTH_OBJ, ground_truth_obj), (ID_OBJ, id_obj)):
        object = cellprofiler.object.Objects()
        if d.shape[1] == 3:
            object.ijv = d
        else:
github CellProfiler / CellProfiler / tests / modules / test_imagemath.py View on Github external
def run_imagemath(images, modify_module_fn=None, measurement=None):
    """Run the ImageMath module, returning the image created

    images - a list of dictionaries. The dictionary has keys:
             pixel_data - image pixel data
             mask - mask for image
             cropping - cropping mask for image
    modify_module_fn - a function of the signature, fn(module)
             that allows the test to modify the module.
    measurement - an image measurement value
    """
    image_set_list = cellprofiler.image.ImageSetList()
    image_set = image_set_list.get_image_set(0)
    module = cellprofiler.modules.imagemath.ImageMath()
    module.set_module_num(1)
    for i, image in enumerate(images):
        pixel_data = image["pixel_data"]
        mask = image.get("mask", None)
        cropping = image.get("cropping", None)
        if i >= 2:
            module.add_image()
        name = "inputimage%s" % i
        module.images[i].image_name.value = name
        img = cellprofiler.image.Image(pixel_data, mask=mask, crop_mask=cropping)
        image_set.add(name, img)
    module.output_image_name.value = "outputimage"
    if modify_module_fn is not None:
        modify_module_fn(module)
github CellProfiler / CellProfiler / tests / modules / test_maskobjects.py View on Github external
assert not isinstance(event, cellprofiler.pipeline.RunExceptionEvent)

    pipeline.add_listener(callback)
    pipeline.add_module(module)

    object_set = cellprofiler.object.ObjectSet()
    io = cellprofiler.object.Objects()
    io.segmented = labels
    object_set.add_objects(io, INPUT_OBJECTS)

    if masking_objects is not None:
        oo = cellprofiler.object.Objects()
        oo.segmented = masking_objects
        object_set.add_objects(oo, MASKING_OBJECTS)

    image_set_list = cellprofiler.image.ImageSetList()
    image_set = image_set_list.get_image_set(0)
    if masking_image is not None:
        mi = cellprofiler.image.Image(masking_image)
        image_set.add(MASKING_IMAGE, mi)

    workspace = cellprofiler.workspace.Workspace(
        pipeline,
        module,
        image_set,
        object_set,
        cellprofiler.measurement.Measurements(),
        image_set_list,
    )
    return workspace, module
github CellProfiler / CellProfiler / tests / modules / test_loaddata.py View on Github external
""".format(
        **{
            "cp_logo_url": tests.modules.cp_logo_url,
            "cp_logo_url_filename": tests.modules.cp_logo_url_filename,
        }
    )
    pipeline, module, filename = make_pipeline(csv_text)
    assert isinstance(module, cellprofiler.modules.loaddata.LoadData)
    m = cellprofiler.measurement.Measurements()
    workspace = cellprofiler.workspace.Workspace(
        pipeline,
        module,
        m,
        cellprofiler.object.ObjectSet(),
        m,
        cellprofiler.image.ImageSetList(),
    )
    assert module.prepare_run(workspace)
    assert (
        m.get_measurement(cellprofiler.measurement.IMAGE, "FileName_DNA", 1)
        == tests.modules.cp_logo_url_filename
    )
    path = m.get_measurement(cellprofiler.measurement.IMAGE, "PathName_DNA", 1)
    assert path == tests.modules.cp_logo_url_folder
    assert (
        m.get_measurement(cellprofiler.measurement.IMAGE, "URL_DNA", 1)
        == tests.modules.cp_logo_url
    )
    assert (
        m[cellprofiler.measurement.IMAGE, "FileName_DNA", 2]
        == tests.modules.cp_logo_url_filename
    )
github CellProfiler / CellProfiler / tests / modules / test_displaydataonimage.py View on Github external
m.add_measurement(OBJECTS_NAME, MEASUREMENT_NAME, numpy.array(measurement))
        y, x = centrosome.cpmorphology.centers_of_labels(labels)
        m.add_measurement(OBJECTS_NAME, "Location_Center_X", x)
        m.add_measurement(OBJECTS_NAME, "Location_Center_Y", y)
        if image is None:
            image = numpy.zeros(labels.shape)
    module.measurement.value = MEASUREMENT_NAME

    pipeline = cellprofiler.pipeline.Pipeline()

    def callback(caller, event):
        assert not isinstance(event, cellprofiler.pipeline.RunExceptionEvent)

    pipeline.add_listener(callback)
    pipeline.add_module(module)
    image_set_list = cellprofiler.image.ImageSetList()
    image_set = image_set_list.get_image_set(0)
    image_set.add(INPUT_IMAGE_NAME, cellprofiler.image.Image(image))

    workspace = cellprofiler.workspace.Workspace(
        pipeline, module, image_set, object_set, m, image_set_list
    )
    return workspace, module
github CellProfiler / CellProfiler / tests / test_module.py View on Github external
def test_add_measurements(self):
        measurements = cellprofiler.measurement.Measurements()

        module = cellprofiler.module.ImageSegmentation()

        module.x_name.value = "Image"

        image = cellprofiler.image.Image(image=numpy.zeros((30, 30)))

        image_set_list = cellprofiler.image.ImageSetList()

        image_set = image_set_list.get_image_set(0)

        image_set.add("Image", image)

        object_set = cellprofiler.object.ObjectSet()

        labels = numpy.zeros((30, 30), dtype=numpy.uint8)

        i, j = numpy.mgrid[-15:15, -7:23]
        labels[i ** 2 + j ** 2 <= 25] = 1

        i, j = numpy.mgrid[-15:15, -22:8]
        labels[i ** 2 + j ** 2 <= 16] = 2

        objects = cellprofiler.object.Objects()