dcnum 0.11.3__py3-none-any.whl → 0.11.5__py3-none-any.whl

tests/test_segm_thresh.py

@@ -1,139 +0,0 @@
-import multiprocessing as mp
-import pathlib
-
-from dcnum import segm
-import h5py
-import numpy as np
-from skimage import morphology
-
-import pytest
-
-from helper_methods import retrieve_data
-
-data_path = pathlib.Path(__file__).parent / "data"
-
-
-def test_segm_thresh_basic():
-    """Basic thresholding segmenter
-
-    The segmenter is equivalent to the old dcevent legacy segmenter with
-    the options legacy:t=-6^bl=0^bi=0^d=1:cle=1^f=1^clo=3
-    (no blur, no binaryops, clear borders, fill holes, closing disk 3).
-    Since in the dcevent pipeline, the data are gated and small objects
-    are removed, we have to do this here manually before comparing mask
-    images.
-    """
-    path = retrieve_data(
-        data_path / "fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip")
-
-    # Get all the relevant information
-    with h5py.File(path) as h5:
-        image = h5["events/image"][:]
-        image_bg = h5["events/image_bg"][:]
-        mask = h5["events/mask"][:]
-        frame = h5["events/frame"][:]
-
-    # Concatenate the masks
-    frame_u, indices = np.unique(frame, return_index=True)
-    image_u = image[indices]
-    image_bg_u = image_bg[indices]
-    mask_u = np.zeros_like(image_u, dtype=bool)
-    for ii, fr in enumerate(frame):
-        idx = np.where(frame_u == fr)[0]
-        mask_u[idx] = np.logical_or(mask_u[idx], mask[ii])
-
-    image_u_c = np.array(image_u, dtype=int) - image_bg_u
-
-    sm = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                        kwargs_mask={"closing_disk": 3})
-    for ii in range(len(frame_u)):
-        labels_seg = sm.segment_frame(image_u_c[ii])
-        mask_seg = np.array(labels_seg, dtype=bool)
-        # Remove small objects, because this is not implemented in the
-        # segmenter class as it would be part of gating.
-        mask_seg = morphology.remove_small_objects(mask_seg, min_size=10)
-        assert np.all(mask_seg == mask_u[ii]), f"masks not matching at {ii}"
-
-
-@pytest.mark.parametrize("worker_type", ["thread", "process"])
-def test_segm_thresh_segment_batch(worker_type):
-    debug = worker_type == "thread"
-    path = retrieve_data(
-        data_path / "fmt-hdf5_cytoshot_full-features_legacy_allev_2023.zip")
-
-    # Get all the relevant information
-    with h5py.File(path) as h5:
-        image = h5["events/image"][:]
-        image_bg = h5["events/image_bg"][:]
-        mask = h5["events/mask"][:]
-        frame = h5["events/frame"][:]
-
-    # Concatenate the masks
-    frame_u, indices = np.unique(frame, return_index=True)
-    image_u = image[indices]
-    image_bg_u = image_bg[indices]
-    mask_u = np.zeros_like(image_u, dtype=bool)
-    for ii, fr in enumerate(frame):
-        idx = np.where(frame_u == fr)[0]
-        mask_u[idx] = np.logical_or(mask_u[idx], mask[ii])
-
-    image_u_c = np.array(image_u, dtype=int) - image_bg_u
-
-    sm = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                        debug=debug,
-                                        kwargs_mask={"closing_disk": 3})
-
-    labels_seg = sm.segment_batch(image_u_c, start=0, stop=5)
-    assert labels_seg is sm.labels_array
-    assert np.all(np.array(labels_seg, dtype=bool) == sm.mask_array)
-    # tell workers to stop
-    sm.join_workers()
-
-    for ii in range(len(frame_u)):
-        mask_seg = np.array(labels_seg[ii], dtype=bool)
-        # Remove small objects, because this is not implemented in the
-        # segmenter class as it would be part of gating.
-        mask_seg = morphology.remove_small_objects(mask_seg, min_size=10)
-        assert np.all(mask_seg == mask_u[ii]), f"masks not matching at {ii}"
-
-
-@pytest.mark.parametrize("worker_type", ["thread", "process"])
-def test_segm_thresh_segment_batch_large(worker_type):
-    debug = worker_type == "thread"
-
-    # Create fake data
-    mask = np.zeros((121, 80, 200), dtype=bool)
-    mask[:, 10:71, 100:161] = morphology.disk(30).reshape(-1, 61, 61)
-    image = -10 * mask
-
-    sm = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                        kwargs_mask={"closing_disk": 3},
-                                        debug=debug)
-
-    labels_seg_1 = np.copy(
-        sm.segment_batch(image, start=0, stop=101))
-
-    assert labels_seg_1.dtype == np.uint16  # uint8 is not enough
-    assert sm.mp_batch_index.value == 0
-    if worker_type == "thread":
-        assert len(sm._mp_workers) == 1
-        assert sm.mp_batch_worker.value == 1
-    else:
-        # This will fail if you have too many CPUs in your system
-        assert len(sm._mp_workers) == mp.cpu_count()
-        # Check whether all processes did their deeds
-        assert sm.mp_batch_worker.value == mp.cpu_count()
-
-    labels_seg_2 = np.copy(
-        sm.segment_batch(image, start=101, stop=121))
-
-    # tell workers to stop
-    sm.join_workers()
-
-    for ii in range(101):
-        mask_seg = np.array(labels_seg_1[ii], dtype=bool)
-        assert np.all(mask_seg == mask[ii]), f"masks not matching at {ii}"
-
-    for jj in range(101, 121):
-        mask_seg = np.array(labels_seg_2[jj - 101], dtype=bool)
-        assert np.all(mask_seg == mask[jj]), f"masks not matching at {jj}"

tests/test_segmenter.py

@@ -1,225 +0,0 @@
-import pathlib
-
-from dcnum import segm
-import numpy as np
-
-data_path = pathlib.Path(__file__).parent / "data"
-
-
-class MockImageData:
-    mask = np.array([
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 0, 1, 0, 0, 0],  # filled, 1
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 1, 1, 1, 1],
-        [0, 0, 0, 0, 0, 1, 1, 1],  # border, 2
-        [0, 0, 0, 0, 0, 1, 1, 1],
-        [0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],  # other, 3
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        ], dtype=bool)
-
-    def get_chunk(self, chunk_index):
-        image = np.array(-(10 + chunk_index) * self.mask, dtype=np.int16)
-        chunk = np.stack([image] * 100, dtype=np.int16)
-        return chunk
-
-
-def test_segmenter_labeled_mask():
-    mask = np.array([
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 0, 1, 0, 0, 0],  # filled, 1
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 1, 1, 1, 1],
-        [0, 0, 0, 0, 0, 1, 1, 1],  # border, 2
-        [0, 0, 0, 0, 0, 1, 1, 1],
-        [0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],  # other, 3
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        ], dtype=bool)
-
-    sm1 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": True,
-                                                      "fill_holes": True,
-                                                      "closing_disk": 0,
-                                                      })
-    labels1 = sm1.segment_frame(-10 * mask)
-    assert np.sum(labels1 != 0) == 21
-    assert len(np.unique(labels1)) == 3  # (bg, filled, other)
-    assert np.sum(labels1 == 1) == 9
-    # due to the relabeling done in `fill_holes`, the index of "other" is "3"
-    assert np.sum(labels1 == 2) == 12
-
-    sm2 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": True,
-                                                      "fill_holes": False,
-                                                      "closing_disk": 0,
-                                                      })
-    labels2 = sm2.segment_frame(-10 * mask)
-    _, l2a, l2b = np.unique(labels2)
-    assert np.sum(labels2 != 0) == 20
-    assert len(np.unique(labels2)) == 3  # (bg, filled, other)
-    assert np.sum(labels2 == l2a) == 8
-    assert np.sum(labels2 == l2b) == 12
-
-    sm3 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": False,
-                                                      "fill_holes": False,
-                                                      "closing_disk": 0,
-                                                      })
-    labels3 = sm3.segment_frame(-10 * mask)
-    assert np.sum(labels3 != 0) == 30
-    assert len(np.unique(labels3)) == 4  # (bg, filled, border, other)
-    assert np.sum(labels3 == 1) == 8
-    assert np.sum(labels3 == 2) == 10
-    assert np.sum(labels3 == 3) == 12
-
-    sm4 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": False,
-                                                      "fill_holes": True,
-                                                      "closing_disk": 0,
-                                                      })
-    labels4 = sm4.segment_frame(-10 * mask)
-    assert np.sum(labels4 != 0) == 31
-    assert len(np.unique(labels4)) == 4  # (bg, filled, border, other)
-    assert np.sum(labels4 == 1) == 9
-    assert np.sum(labels4 == 2) == 10
-    assert np.sum(labels4 == 3) == 12
-
-
-def test_segmenter_labeled_mask_closing_disk():
-    mask = np.array([
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 1, 0, 1, 0, 0, 0, 0],  # filled, 1
-        [0, 0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 1, 1, 1, 1],
-        [0, 0, 0, 0, 0, 0, 1, 1, 1],  # border, 2
-        [0, 0, 0, 0, 0, 0, 0, 0, 1],
-        [0, 0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 1, 0, 0, 1, 1, 0, 0],  # other, 3
-        [0, 0, 1, 0, 0, 0, 1, 0, 0],
-        [0, 0, 1, 0, 0, 0, 1, 0, 0],
-        [0, 0, 1, 1, 1, 1, 1, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0, 0],
-        ], dtype=bool)
-
-    sm1 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": True,
-                                                      "fill_holes": True,
-                                                      "closing_disk": 1,
-                                                      })
-    labels1 = sm1.segment_frame(-10 * mask)
-    assert np.sum(labels1 != 0) == 32
-    assert len(np.unique(labels1)) == 3  # (bg, filled, other)
-    assert np.sum(labels1 == 1) == 9
-    # due to the relabeling done in `fill_holes`, the index of "other" is "3"
-    assert np.sum(labels1 == 2) == 23
-
-    sm2 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": True,
-                                                      "fill_holes": False,
-                                                      "closing_disk": 1,
-                                                      })
-    labels2 = sm2.segment_frame(-10 * mask)
-    _, l2a, l2b = np.unique(labels2)
-    assert np.sum(labels2 != 0) == 27
-    assert len(np.unique(labels2)) == 3  # (bg, filled, other)
-    assert np.sum(labels2 == l2a) == 9
-    assert np.sum(labels2 == l2b) == 18
-
-    sm3 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": False,
-                                                      "fill_holes": False,
-                                                      "closing_disk": 1,
-                                                      })
-    labels3 = sm3.segment_frame(-10 * mask)
-    assert np.sum(labels3 != 0) == 35
-    assert len(np.unique(labels3)) == 4  # (bg, filled, border, other)
-    assert np.sum(labels3 == 1) == 9
-    assert np.sum(labels3 == 2) == 8
-    assert np.sum(labels3 == 3) == 18
-
-    sm4 = segm.segm_thresh.SegmentThresh(thresh=-6,
-                                         kwargs_mask={"clear_border": False,
-                                                      "fill_holes": True,
-                                                      "closing_disk": 1,
-                                                      })
-    labels4 = sm4.segment_frame(-10 * mask)
-    assert np.sum(labels4 != 0) == 40
-    assert len(np.unique(labels4)) == 4  # (bg, filled, border, other)
-    assert np.sum(labels4 == 1) == 9
-    assert np.sum(labels4 == 2) == 8
-    assert np.sum(labels4 == 3) == 23
-
-
-def test_segmenter_labeled_mask_fill_holes_int32():
-    mask = np.array([
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 0, 1, 0, 0, 0],  # filled, 1
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        [0, 0, 0, 0, 1, 1, 1, 1],
-        [0, 0, 0, 0, 0, 1, 1, 1],  # border, 2
-        [0, 0, 0, 0, 0, 1, 1, 1],
-        [0, 1, 1, 1, 0, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],  # other, 3
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 1, 1, 1, 0, 0, 0],
-        [0, 0, 0, 0, 0, 0, 0, 0],
-        ], dtype=bool)
-
-    sm1 = segm.segm_thresh.SegmentThresh(thresh=-6)
-    labels = np.array(sm1.segment_frame(-10 * mask), dtype=np.int64)
-    # sanity checks
-    assert labels.dtype == np.int64
-    assert labels.dtype != np.int32
-    labels_2 = sm1.process_mask(labels,
-                                clear_border=False,
-                                fill_holes=True,
-                                closing_disk=False)
-    assert np.allclose(labels, labels_2)
-    assert labels_2.dtype == np.int32
-
-
-def test_segmenter_segment_chunk():
-    with segm.segm_thresh.SegmentThresh(thresh=-12, debug=True) as sm:
-        image_data = MockImageData()
-        labels_1 = np.copy(sm.segment_chunk(image_data, 0))  # below threshold
-        assert sm.image_array.min() == -10
-        labels_2 = np.copy(sm.segment_chunk(image_data, 10))  # above threshold
-        assert sm.image_array.min() == -20
-        assert np.all(labels_1 == 0)
-        assert not np.all(labels_2 == 0)
-
-
-def test_cpu_segmenter_getsetstate():
-    sm1 = segm.segm_thresh.SegmentThresh(thresh=-12, debug=True)
-    with segm.segm_thresh.SegmentThresh(thresh=-12, debug=True) as sm2:
-        image_data = MockImageData()
-        # Do some processing so that we have workers
-        sm2.segment_chunk(image_data, 0)
-        # get the state
-        state = sm2.__getstate__()
-        # set the state
-        sm1.__setstate__(state)
-        # and here we test for the raw data that was transferred
-        assert not np.all(sm1.image_array == sm2.image_array)
-        assert np.all(sm1.mp_image_raw == sm2.mp_image_raw)

tests/test_write_deque_writer_thread.py

@@ -1,42 +0,0 @@
-import collections
-import pathlib
-
-import h5py
-
-from dcnum import write
-
-from helper_methods import retrieve_data
-
-data_path = pathlib.Path(__file__).parent / "data"
-
-
-def test_writer_thread_basic():
-    path = retrieve_data(data_path /
-                         "fmt-hdf5_cytoshot_full-features_2023.zip")
-    path_wrt = path.with_name("written.hdf5")
-    dq = collections.deque()
-
-    wrthr = write.DequeWriterThread(path_out=path_wrt, dq=dq)
-    wrthr.start()
-
-    with h5py.File(path) as h5:
-        deform = h5["events"]["deform"][:]
-        image = h5["events"]["image"][:]
-
-        dq.append(("deform", deform))
-        dq.append(("deform", deform))
-        dq.append(("deform", deform[:10]))
-
-        dq.append(("image", image))
-        dq.append(("image", image))
-        dq.append(("image", image[:10]))
-
-    wrthr.finished_when_queue_empty()
-    wrthr.join()
-
-    with h5py.File(path_wrt) as ho:
-        events = ho["events"]
-        size = deform.shape[0]
-        assert events["deform"].shape[0] == 2*size + 10
-        assert events["image"].shape[0] == 2 * size + 10
-        assert events["image"].shape[1:] == image.shape[1:]

tests/test_write_writer.py

@@ -1,33 +0,0 @@
-import pathlib
-
-import h5py
-
-from dcnum import write
-
-from helper_methods import retrieve_data
-
-data_path = pathlib.Path(__file__).parent / "data"
-
-
-def test_writer_basic():
-    path = retrieve_data(data_path /
-                         "fmt-hdf5_cytoshot_full-features_2023.zip")
-    path_wrt = path.with_name("written.hdf5")
-    with h5py.File(path) as h5, write.HDF5Writer(path_wrt) as hw:
-        deform = h5["events"]["deform"][:]
-        image = h5["events"]["image"][:]
-
-        hw.store_feature_chunk(feat="deform", data=deform)
-        hw.store_feature_chunk(feat="deform", data=deform)
-        hw.store_feature_chunk(feat="deform", data=deform[:10])
-
-        hw.store_feature_chunk(feat="image", data=image)
-        hw.store_feature_chunk(feat="image", data=image)
-        hw.store_feature_chunk(feat="image", data=image[:10])
-
-    with h5py.File(path_wrt) as ho:
-        events = ho["events"]
-        size = deform.shape[0]
-        assert events["deform"].shape[0] == 2*size + 10
-        assert events["image"].shape[0] == 2 * size + 10
-        assert events["image"].shape[1:] == image.shape[1:]