def test_image_basic():
ds = new_dataset(retrieve_data(example_data_sets[1]))
# Transition image
assert np.allclose(ds["image"][0], 0)
# Real image
assert np.allclose(np.average(ds["image"][1]), 45.1490478515625)
cleanup()
def test_078hierarchy2():
"""
In 0.7.8, each dataset gets a unique identifier that is independent
of the data it holds. Therefore, two identical datasets (same filters,
same hierarchy parents) will always have a different identifier.
"""
analysis = compatibility_task("session_v0.7.8_hierarchy2.zmso")
mms = analysis.measurements
assert mms[0].title == "parent"
assert mms[1].title == "child1"
assert mms[2].title == "child2"
assert mms[3].title == "grandchild1a"
assert mms[4].title == "grandchild1b"
assert mms[5].title == "grandchild2a"
assert len(mms[0]) == 44
assert len(mms[1]) == 37
assert len(mms[2]) == 37
assert len(mms[3]) == 22
assert len(mms[4]) == 22
assert len(mms[5]) == 15
assert mms[0].identifier == "mm-tdms_8a43345"
assert mms[1].identifier == "mm-hierarchy_b7a2c21"
assert mms[2].identifier == "mm-hierarchy_bbcb5a8"
assert mms[3].identifier == "mm-hierarchy_4c7d883"
assert mms[4].identifier == "mm-hierarchy_91b0b96"
assert mms[5].identifier == "mm-hierarchy_38d374e"
cleanup()
def test_area_ratio():
ds = dclab.new_dataset(retrieve_data("rtdc_data_traces_video.zip"))
comp_ratio = ds["area_ratio"]
# The convex area is always >= the raw area
assert np.all(comp_ratio >= 1)
assert np.allclose(comp_ratio[0], 1.0196464)
cleanup()
def test_time():
ds = dclab.new_dataset(retrieve_data("rtdc_data_minimal.zip"))
tt = ds["time"]
assert tt[0] == 0
assert np.allclose(tt[1], 0.0385)
assert np.all(np.diff(tt) > 0)
cleanup()
def test_config():
ds = new_dataset(retrieve_data("rtdc_data_hdf5_contour_image_trace.zip"))
assert ds.config["setup"]["channel width"] == 30
assert ds.config["setup"]["chip region"].lower() == "channel"
assert ds.config["setup"]["flow rate"] == 0.16
assert ds.config["imaging"]["pixel size"] == 0.34
cleanup()
def test_compatibility_minimal():
ds = new_dataset(retrieve_data("rtdc_data_minimal.zip"))
assert ds.config["setup"]["channel width"] == 20
assert ds.config["setup"]["chip region"].lower() == "channel"
assert ds.config["setup"]["flow rate"] == 0.12
assert ds.config["imaging"]["pixel size"] == 0.34
cleanup()
def test_trace():
ds = new_dataset(retrieve_data("rtdc_data_hdf5_contour_image_trace.zip"))
assert len(ds["trace"]) == 2
assert ds["trace"]["fl1_raw"].shape == (5, 100)
assert np.allclose(np.average(
ds["trace"]["fl1_median"][0]), 0.027744706519425219)
cleanup()
def test_078hierarchy2():
"""
In 0.7.8, each dataset gets a unique identifier that is independent
of the data it holds. Therefore, two identical datasets (same filters,
same hierarchy parents) will always have a different identifier.
"""
analysis = compatibility_task("session_v0.7.8_hierarchy2.zmso")
mms = analysis.measurements
assert mms[0].title == "parent"
assert mms[1].title == "child1"
assert mms[2].title == "child2"
assert mms[3].title == "grandchild1a"
assert mms[4].title == "grandchild1b"
assert mms[5].title == "grandchild2a"
assert len(mms[0]) == 44
assert len(mms[1]) == 37
assert len(mms[2]) == 37
assert len(mms[3]) == 22
assert len(mms[4]) == 22
assert len(mms[5]) == 15
assert mms[0].identifier == "mm-tdms_8a43345"
assert mms[1].identifier == "mm-hierarchy_b7a2c21"
assert mms[2].identifier == "mm-hierarchy_bbcb5a8"
assert mms[3].identifier == "mm-hierarchy_4c7d883"
assert mms[4].identifier == "mm-hierarchy_91b0b96"
assert mms[5].identifier == "mm-hierarchy_38d374e"
cleanup()
def test_aspect():
# Aspect ratio of the data
ds = dclab.new_dataset(retrieve_data("rtdc_data_traces_video_bright.zip"))
aspect = ds["aspect"]
assert np.sum(aspect > 1) == 904
assert np.sum(aspect < 1) == 48
cleanup()
def test_077hierarchy2():
analysis = compatibility_task("session_v0.7.7_hierarchy2.zmso")
mms = analysis.measurements
assert mms[0].title == "original data"
assert mms[1].title == "child1"
assert mms[2].title == "grandchild1a"
assert mms[3].title == "child2"
assert mms[4].title == "grandchild2a"
assert len(mms[0]) == 44
assert len(mms[1]) == 37
assert len(mms[2]) == 14
assert len(mms[3]) == 37
assert len(mms[4]) == 19
# Backwards compatibility: identifiers are saved in session and not anymore
# computed from session hashes in 0.7.8. Using the `key` of the measurement
# allows to assign new unique identifiers.
assert mms[0].identifier == "1_mm-tdms_92601489292dc9bf9fc040f87d9169c0"
assert mms[
1].identifier == "2_mm-hierarchy_033dc4bc9d581bcfcdb9f153105f3b15"
assert mms[
2].identifier == "3_mm-hierarchy_119eb293afc12ad63c4b8f8db962d0e3"
assert mms[
3].identifier == "4_mm-hierarchy_c30bc68d7339267d61c2e0382ae8ba26"
assert mms[
4].identifier == "5_mm-hierarchy_3bed98d737cd70f1c46d5ab44cb627a8"
cleanup()
def test_0basic():
ds = dclab.new_dataset(retrieve_data(example_data_sets[1]))
for cc in ['fl1_pos',
'frame',
'size_x',
'size_y',
'contour',
'area_cvx',
'circ',
'image',
'trace',
'fl1_width',
'nevents',
'pos_x',
'pos_y',
'fl1_area',
'fl1_max',
]:
assert cc in ds
# ancillaries
for cc in ["deform",
"area_um",
"aspect",
"frame",
"index",
"time",
]:
assert cc in ds
cleanup()
def test_075hierarchy2():
analysis = compatibility_task("session_v0.7.5_hierarchy2.zmso")
mms = analysis.measurements
assert np.sum(mms[0]._filter) == len(mms[1])
assert np.sum(mms[1]._filter) == len(mms[2])
assert np.sum(mms[0]._filter) == 17
assert np.sum(mms[2]._filter) == 4
cleanup()
def test_trace_basic():
ds = new_dataset(retrieve_data(example_data_sets[1]))
msg = "traces should not be loaded into memory before first access"
assert ds["trace"].__repr__().count("<not loaded into memory>"), msg
assert len(ds["trace"]) == 2
assert np.allclose(np.average(
ds["trace"]["fl1_median"][0]), 287.08999999999997)
cleanup()
def test_trace_methods():
ds = new_dataset(retrieve_data(example_data_sets[1]))
for k in list(ds["trace"].keys()):
assert k in dclab.definitions.FLUOR_TRACES
for k in ds["trace"]:
assert k in dclab.definitions.FLUOR_TRACES
assert ds["trace"].__repr__().count("<loaded into memory>")
cleanup()
def test_075hierarchy2():
analysis = compatibility_task("session_v0.7.5_hierarchy2.zmso")
mms = analysis.measurements
assert np.sum(mms[0]._filter) == len(mms[1])
assert np.sum(mms[1]._filter) == len(mms[2])
assert np.sum(mms[0]._filter) == 17
assert np.sum(mms[2]._filter) == 4
cleanup()
def test_inert_ratio_raw():
ds = new_dataset(retrieve_data("rtdc_data_hdf5_mask_contour.zip"))
raw = ir.get_inert_ratio_raw(cont=ds["contour"])
ref = np.array([4.25854232, 1.22342663, 4.64971179, 1.70914857,
3.62797492, 1.51502192, 2.74757573, 1.79841136])
assert np.allclose(ref, raw, rtol=0, atol=5e-9)
cleanup()
def test_076hierarchy2():
analysis = compatibility_task("session_v0.7.6_hierarchy2.zmso")
mms = analysis.measurements
assert mms[3].title == "rtdc_data_traces_video - M1_child_child_child"
assert len(mms[0]) == 44
assert len(mms[1]) == 32
assert len(mms[2]) == 12
assert len(mms[3]) == 9
cleanup()
def test_hdf5():
path = retrieve_data("rtdc_data_hdf5_contour_image_trace.zip")
assert meta_tool.get_chip_region(path) == "channel"
assert meta_tool.get_event_count(path) == 5
assert meta_tool.get_flow_rate(path) == .16
assert meta_tool.get_run_index(path) == 1
assert meta_tool.get_sample_name(path) == "artificial test data"
assert meta_tool.verify_dataset(path)
cleanup()
def test_tdms():
path = retrieve_data("rtdc_data_minimal.zip")
assert meta_tool.get_chip_region(path) == "channel"
assert meta_tool.get_event_count(path) == 156
assert meta_tool.get_flow_rate(path) == .12
assert meta_tool.get_run_index(path) == 1
assert "rtdc_data_minimal.zip" in meta_tool.get_sample_name(path)
assert meta_tool.verify_dataset(path)
cleanup()
def test_076hierarchy2():
analysis = compatibility_task("session_v0.7.6_hierarchy2.zmso")
mms = analysis.measurements
assert mms[3].title == "rtdc_data_traces_video - M1_child_child_child"
assert len(mms[0]) == 44
assert len(mms[1]) == 32
assert len(mms[2]) == 12
assert len(mms[3]) == 9
cleanup()
def test_image_out_of_bounds():
ds = new_dataset(retrieve_data(example_data_sets[1]))
try:
ds["image"][5]
except IndexError:
pass
else:
raise ValueError("IndexError should have been raised!")
cleanup()
def test_hdf5():
path = retrieve_data("rtdc_data_hdf5_contour_image_trace.zip")
assert meta_tool.get_chip_region(path) == "channel"
assert meta_tool.get_event_count(path) == 5
assert meta_tool.get_flow_rate(path) == .16
assert meta_tool.get_run_index(path) == 1
assert meta_tool.get_sample_name(path) == "artificial test data"
assert meta_tool.verify_dataset(path)
cleanup()
def test_mask_basic():
ds = new_dataset(retrieve_data(example_data_sets[1]))
assert len(ds["mask"]) == 12
# Test mask computation by averaging brightness and comparing to
# the ancillary feature "bright_avg".
bavg1 = ds["bright_avg"][1]
bavg2 = np.mean(ds["image"][1][ds["mask"][1]])
assert np.allclose(bavg1, bavg2), "mask is correctly computed from contour"
cleanup()
def test_tdms():
path = retrieve_data("rtdc_data_minimal.zip")
assert meta_tool.get_chip_region(path) == "channel"
assert meta_tool.get_event_count(path) == 156
assert meta_tool.get_flow_rate(path) == .12
assert meta_tool.get_run_index(path) == 1
assert "rtdc_data_minimal.zip" in meta_tool.get_sample_name(path)
assert meta_tool.verify_dataset(path)
cleanup()
def test_avi_export():
ds = new_dataset(retrieve_data(example_data_sets[1]))
edest = tempfile.mkdtemp()
f1 = join(edest, "test.avi")
ds.export.avi(path=f1)
assert os.stat(
f1)[6] > 1e4, "Resulting file to small, Something went wrong!"
shutil.rmtree(edest, ignore_errors=True)
cleanup()
def test_tdms_avi():
path = retrieve_data("rtdc_data_traces_video.zip")
assert meta_tool.get_chip_region(path) == "channel"
# this is the number of frames in the video file
assert meta_tool.get_event_count(path) == 2
assert meta_tool.get_flow_rate(path) == .16
assert meta_tool.get_run_index(path) == 1
assert "rtdc_data_traces_video.zip" in meta_tool.get_sample_name(path)
assert meta_tool.verify_dataset(path)
cleanup()
def test_compatibility_channel_width():
# At some point, "Channel width" was repleaced by "Channel width [um]"
path = retrieve_data("rtdc_data_minimal.zip")
para = path.parent / "M1_para.ini"
pardata = para.read_text()
pardata = pardata.replace("Channel width = 20\n", "Channel width = 34\n")
para.write_text(pardata)
ds = new_dataset(path)
assert ds.config["setup"]["channel width"] == 34
cleanup()
def test_trace_import_fail():
# make sure undefined trace data does not raise an error
tdms_path = retrieve_data(example_data_sets[1])
dclab.definitions.FLUOR_TRACES.append("peter")
dclab.rtdc_dataset.fmt_tdms.naming.tr_data_map["peter"] = [u'ukwn', u'ha']
new_dataset(tdms_path)
# clean up
dclab.rtdc_dataset.fmt_tdms.naming.tr_data_map.pop("peter")
dclab.definitions.FLUOR_TRACES.pop(-1)
cleanup()
def test_simple_bright():
ds = new_dataset(retrieve_data("rtdc_data_traces_video_bright.zip"))
for ii in range(2, 7):
# This stripped dataset has only 7 video frames / contours
image = ds["image"][ii]
mask = ds["mask"][ii]
avg, std = get_bright(mask=mask, image=image, ret_data="avg,sd")
assert np.allclose(avg, ds["bright_avg"][ii])
assert np.allclose(std, ds["bright_sd"][ii])
cleanup()
def test_pixel_size():
path = retrieve_data("rtdc_data_minimal.zip")
para = path.parent / "M1_para.ini"
data = para.open("r").read()
newdata = data.replace("Pix Size = 0.340000", "Pix Size = 0.120000")
with para.open("w") as fd:
fd.write(newdata)
ds = new_dataset(path)
assert ds.config["imaging"]["pixel size"] == 0.12
cleanup()
def test_tdms_avi():
path = retrieve_data("rtdc_data_traces_video.zip")
assert meta_tool.get_chip_region(path) == "channel"
# this is the number of frames in the video file
assert meta_tool.get_event_count(path) == 2
assert meta_tool.get_flow_rate(path) == .16
assert meta_tool.get_run_index(path) == 1
assert "rtdc_data_traces_video.zip" in meta_tool.get_sample_name(path)
assert meta_tool.verify_dataset(path)
cleanup()
def test_compatibility_shapein201():
ds = new_dataset(retrieve_data("rtdc_data_shapein_v2.0.1.zip"))
assert ds.config["setup"]["channel width"] == 20
assert ds.config["setup"]["chip region"].lower() == "channel"
assert ds.config["setup"]["software version"] == "ShapeIn 2.0.1"
assert ds.config["imaging"]["pixel size"] == 0.34
assert ds.config["imaging"]["flash duration"] == 2
assert ds.config["experiment"]["date"] == "2017-10-12"
assert ds.config["experiment"]["time"] == "12:54:31"
cleanup()
def test_unicode_paths():
path = retrieve_data(example_data_sets[1])
path = pathlib.Path(path)
pp = path.parent
# create a unicode name
pp2 = pathlib.Path(tempfile.mktemp(prefix="dclàb_tést_asgård_únícodè"))
pp.rename(pp2)
ds = new_dataset(pp2 / path.name)
ds.__repr__()
shutil.rmtree(str(pp2), ignore_errors=True)
cleanup()
def test_083():
"""Major version test
"""
analysis = compatibility_task("session_v0.8.3.zmso")
mms = analysis.measurements
mm = mms[0]
assert len(mm) == 44
assert np.sum(mm.filter.all) == 30
# In the configuration file, this is set to "False" by accident.
assert mm.config["filtering"]["limit events"] == 0
cleanup()
def test_080():
"""Major version test
"""
analysis = compatibility_task("session_v0.8.0.zmso")
mms = analysis.measurements
assert mms[0].title == 'rtdc_data_traces_video - M1'
assert mms[-1].title == 'rtdc_data_traces_video - M1_child_child'
assert len(mms[-1]) == 3
assert len(mms) == 5
assert mms[0].config["plotting"]["axis y"] == "volume"
cleanup()
def test_083():
"""Major version test
"""
analysis = compatibility_task("session_v0.8.3.zmso")
mms = analysis.measurements
mm = mms[0]
assert len(mm) == 44
assert np.sum(mm.filter.all) == 30
# In the configuration file, this is set to "False" by accident.
assert mm.config["filtering"]["limit events"] == 0
cleanup()
def test_080():
"""Major version test
"""
analysis = compatibility_task("session_v0.8.0.zmso")
mms = analysis.measurements
assert mms[0].title == 'rtdc_data_traces_video - M1'
assert mms[-1].title == 'rtdc_data_traces_video - M1_child_child'
assert len(mms[-1]) == 3
assert len(mms) == 5
assert mms[0].config["plotting"]["axis y"] == "volume"
cleanup()
def test_inert_ratio_prnc():
# Brightness of the image
ds = dclab.new_dataset(retrieve_data("rtdc_data_traces_video_bright.zip"))
# This will cause a zero-padding warning:
prnc = ds["inert_ratio_prnc"]
raw = ds["inert_ratio_raw"]
idcompare = ~np.isnan(prnc)
# ignore first event (no image data)
idcompare[0] = False
diff = (prnc - raw)[idcompare]
# only compare the first valid event which seems to be quite close
assert np.allclose(diff[0], 0, atol=1.2e-3, rtol=0)
cleanup()
def test_config_save_load():
# Download and extract data
tdms_path = retrieve_data(example_data_sets[0])
ds = new_dataset(tdms_path)
cfg_file = tempfile.mktemp(prefix="test_dclab_rtdc_config_")
ds.config.save(cfg_file)
loaded = Configuration(files=[cfg_file])
assert equals(loaded, ds.config)
cleanup()
try:
os.remove(cfg_file)
except OSError:
pass
def test_084_pre_isoelastics_conversion():
"""Manual filters for hierarchy children are stored in session
"""
analysis = compatibility_task("session_v0.7.5_hierarchy2.zmso")
mms = analysis.measurements
# isoelastics = True
assert mms[0].config["plotting"]["isoelastics"] == "legacy"
analysis = compatibility_task("session_v0.8.0.zmso")
mms = analysis.measurements
# isoelastics = False
assert mms[0].config["plotting"]["isoelastics"] == "not shown"
cleanup()
def test_078inertratio():
"""
In dclab commit 41bf38e74e4d7dbf25c7d4c37214674b7ea242d6, the column
"inert_ratio" was renamed to "inert_ratio_cvx". The conversion of the
corresponding session config values is done starting ShapeOut 0.7.9.
"""
analysis = compatibility_task("session_v0.7.8_hierarchy2.zmso")
mms = analysis.measurements
assert "inert_ratio_cvx min" in mms[0].config["filtering"]
assert "inert_ratio_cvx max" in mms[0].config["filtering"]
assert "inert_ratio_raw min" in mms[0].config["filtering"]
assert "inert_ratio_raw max" in mms[0].config["filtering"]
assert "inert_ratio min" not in mms[0].config["filtering"]
assert "inert_ratio max" not in mms[0].config["filtering"]
cleanup()
def test_084_manhierarchy():
"""Manual filters for hierarchy children are stored in session
"""
analysis = compatibility_task("session_v0.8.4_hierarchy_filtman.zmso")
mms = analysis.measurements
assert mms[0].title == '0000_SessionTest - M1'
assert mms[1].title == '0000_SessionTest - M1_child'
# check basic filter settings
assert len(mms[1]) == 37
assert not mms[1].filter.manual[26]
# make hidden manual filter visible
mms[0].config["filtering"]["enable filters"] = False
mms[1].apply_filter()
assert len(mms[1]) == 44
assert not mms[1].filter.manual[7]
assert not mms[1].filter.manual[32]
cleanup()
def test_rw_basic():
# Create a session with a few datasets
f1 = retrieve_data("rtdc_data_traces_video.zip")
f2 = retrieve_data("rtdc_data_minimal.zip")
an = Analysis([f1, f2])
msave = an.measurements
_fd, fsave = tempfile.mkstemp(suffix=".zsmo",
prefix="shapeout_test_session_")
rw.save(path=fsave, rtdc_list=msave)
mload = rw.load(fsave)
assert mload[0].identifier == msave[0].identifier
assert mload[1].identifier == msave[1].identifier
cleanup()
try:
os.remove(fsave)
except OSError:
pass
def test_polygon():
"""
In versions before 0.7.6, polygons in dclab were exported with
other column names.
"""
sdir, _path = extract_session("session_v0.6.0.zmso")
pfile = op.join(sdir, "PolygonFilters.poly")
# conversion
outfile = conversion.convert_polygon(
pfile,
# pretend we don't know the version
version=None,
)
# load polygon file
pf = dclab.PolygonFilter(filename=outfile)
assert pf.axes == (u'area_um', u'deform')
cleanup()
try:
outfile.unlink()
except OSError:
pass
def test_070():
analysis = compatibility_task("session_v0.7.0.zmso")
mm = analysis.measurements[0]
assert len(mm) == 44
assert np.sum(mm._filter) == 12
cleanup()
def test_verify():
path = retrieve_data("rtdc_data_minimal.zip")
(path.parent / "M1_camera.ini").unlink()
assert not meta_tool.verify_dataset(path)
cleanup()
def test_tdms_avi2():
path = retrieve_data("rtdc_data_traces_video.zip")
# delete avi file and get event count from tdms file
(path.parent / "M1_imaq.avi").unlink()
assert meta_tool.verify_dataset(path)
cleanup()
def tearDown(self):
cleanup()
