def test_reassignment_of_tracename(self):
filename = "../resources/traces/Trace.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.tracename = self.file_name
self.assertEqual(trace.get_tracename(), self.file_name)
self.assertEqual(trace.get_savename(dir_to_join=self.file_dir),
self.file_path)
def test_load_trace_from_ascii_specified_bleach(self):
filename = "../resources/traces/TraceNoAA.txt"
trace = TraceContainer(filename)
self.assertTrue(trace.load_successful)
self.assertIsInstance(trace.acc.int, np.ndarray)
self.assertIsInstance(trace.grn.int, np.ndarray)
self.assertIsInstance(trace.red.int, np.ndarray)
self.assertEqual(
(57, None, 57), trace.get_bleaches()
) # expect bleach to propagate all channels
def test_load_trace_from_dat(self):
filename = "../resources/traces/kinsoftTrace.dat"
trace = TraceContainer(filename)
self.assertTrue(trace.load_successful)
self.assertIsInstance(trace.acc.int, np.ndarray)
self.assertIsInstance(trace.grn.int, np.ndarray)
self.assertIsInstance(trace.red.int, np.ndarray)
self.assertTrue(np.isnan(trace.red.int[0]))
def newTraceFromVideo(self, n) -> TraceContainer:
"""
Shortcut to obtain trace, and create a new one if it doesn't exist.
"""
tracename = self.currName + "_" + str(n)
if tracename not in self.data.traces:
self.data.traces[tracename] = TraceContainer(filename=tracename,
video=self.currName,
n=n)
return self.data.traces[tracename]
def test_save_and_load_trace(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/fiddler_3dim_0.txt"
trace = TraceContainer(filename)
trace.tracename = self.file_path
trace.export_trace_to_txt()
trace2 = TraceContainer(self.file_path)
np.testing.assert_array_almost_equal(trace.grn.int, trace2.grn.int)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
def test_save_and_load_trace(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/Trace.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.tracename = self.file_name
trace.export_trace_to_txt(dir_to_join=self.file_dir)
trace2 = TraceContainer(self.file_path, loaded_from_ascii=True)
self.assertTrue(trace2.load_successful)
np.testing.assert_array_almost_equal(trace.grn.int, trace2.grn.int)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
def test_save_and_load_trace_dat(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/kinsoftTrace.dat"
trace = TraceContainer(filename)
trace.tracename = self.file_path
trace.export_trace_to_txt()
trace2 = TraceContainer(self.file_path)
np.testing.assert_allclose(trace.grn.int, trace2.grn.int, rtol=1e-06)
np.testing.assert_allclose(trace.acc.int, trace2.acc.int, rtol=1e-06)
np.testing.assert_allclose(trace.red.int, trace2.red.int, rtol=1e-06)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
self.assertEqual(trace.n, trace2.n)
def test_save_and_load_trace_dat(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/kinsoftTrace.dat"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.tracename = self.file_name
trace.export_trace_to_txt(dir_to_join=self.file_dir)
trace2 = TraceContainer(self.file_path, loaded_from_ascii=True)
self.assertTrue(trace2.load_successful)
self.assertEqual(type(trace.grn.int), type(trace2.grn.int))
self.assertEqual(type(trace.acc.int), type(trace2.acc.int))
self.assertEqual(type(trace.red.int), type(trace2.red.int))
np.testing.assert_allclose(trace.grn.int, trace2.grn.int, rtol=1e-06)
np.testing.assert_allclose(trace.acc.int, trace2.acc.int, rtol=1e-06)
np.testing.assert_allclose(trace.red.int, trace2.red.int, rtol=1e-06)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
self.assertEqual(trace.n, trace2.n)
def test_reducing_trace_save_and_load(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/fiddler_3dim_0.txt"
trace = TraceContainer(filename)
trace.red.int[:] = None
trace.red.bg[:] = None
trace.stoi[:] = None
trace.tracename = self.file_path
trace.export_trace_to_txt()
trace2 = TraceContainer(self.file_path)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
np.testing.assert_allclose(trace.grn.int, trace2.grn.int)
np.testing.assert_allclose(trace.grn.bg, trace2.grn.bg)
np.testing.assert_allclose(trace.acc.int, trace2.acc.int)
np.testing.assert_allclose(trace.acc.bg, trace2.acc.bg)
np.testing.assert_allclose(trace.red.int, trace2.red.int)
np.testing.assert_allclose(trace.red.bg, trace2.red.bg)
np.testing.assert_allclose(trace.stoi, trace2.stoi)
def test_reducing_trace_save_and_load(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/Trace.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.red.int[:] = None
trace.red.bg[:] = None
trace.stoi[:] = None
trace.tracename = self.file_name
trace.export_trace_to_txt(dir_to_join=self.file_dir)
trace2 = TraceContainer(self.file_path, loaded_from_ascii=True)
self.assertTrue(trace2.load_successful)
self.assertEqual(trace.first_bleach, trace2.first_bleach)
np.testing.assert_allclose(trace.grn.int, trace2.grn.int)
np.testing.assert_allclose(trace.grn.bg, trace2.grn.bg)
np.testing.assert_allclose(trace.acc.int, trace2.acc.int)
np.testing.assert_allclose(trace.acc.bg, trace2.acc.bg)
np.testing.assert_allclose(trace.red.int, trace2.red.int)
np.testing.assert_allclose(trace.red.bg, trace2.red.bg)
np.testing.assert_allclose(trace.stoi, trace2.stoi)
def test_reducing_trace_calculating_fret(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/fiddler_3dim_0.txt"
trace = TraceContainer(filename)
trace.red.int[:] = None
trace.red.bg[:] = None
trace.stoi[:] = None
df = trace.get_export_df()
trace.fret[:] = None
trace.savename = self.file_path
trace.export_trace_to_txt(keep_nan_columns=False)
trace2 = TraceContainer(self.file_path)
df2 = trace2.get_export_df()
np.testing.assert_array_almost_equal(df["E"], df2["E"])
def generateTraces(self, examples: bool):
"""Generate traces to show in the GUI (examples) or for export"""
n_traces = self.n_examples if examples else self.n_traces
if n_traces > 50:
# every number of traces gets 20 updates in total
# but closes if less
update_every_nth = n_traces // 20
progressbar = ProgressBar(
parent=self, loop_len=n_traces / update_every_nth
)
else:
update_every_nth = None
progressbar = None
if examples:
self.data.example_traces.clear()
else:
self.data.simulated_traces.clear()
df = lib.math.generate_traces(
n_traces=n_traces,
aa_mismatch=self.aa_mismatch,
state_means=self.fret_means,
min_state_diff=self.min_fret_diff,
random_k_states_max=self.max_random_states,
max_aggregate_size=self.max_aggregate_size,
aggregation_prob=self.aggregate_prob,
scramble_prob=self.scramble_prob,
scramble_decouple_prob=self.scramble_decouple_prob,
trace_length=self.trace_len,
trans_prob=self.transition_prob,
blink_prob=self.blinking_prob,
bleed_through=self.bleed_through,
noise=self.noise,
D_lifetime=self.donor_lifetime,
A_lifetime=self.acceptor_lifetime,
au_scaling_factor=self.scaling_factor,
falloff_prob=self.fall_off_prob,
falloff_lifetime=self.fall_off_lifetime,
discard_unbleached=False,
progressbar_callback=progressbar,
callback_every=update_every_nth,
return_matrix=False,
reduce_memory=False,
run_headless_parallel=False,
merge_state_labels=True,
)
df.index = np.arange(0, len(df), 1) // int(self.trace_len)
for n, (idx, trace_df) in enumerate(df.groupby(df.index)):
self.data.simulated_traces[idx] = TraceContainer(
filename="trace_{}.txt".format(idx),
loaded_from_ascii=False,
n=idx,
)
self.getTrace(idx).set_from_df(df=trace_df)
if progressbar is not None:
progressbar.close()
def openFile(self, *args):
"""
Loads ASCII files directly into the TraceWindow.
"""
directory = self.getLastOpenedDir()
filenames, selectedFilter = QFileDialog.getOpenFileNames(
self,
caption="Open File",
filter="Trace files (*.txt *.dat)",
directory=directory,
)
if len(filenames) != 0:
select_top_row = True if len(self.data.traces) == 0 else False
update_every_n = int(10) if len(filenames) > 10 else int(2)
progressbar = ProgressBar(loop_len=len(filenames) / update_every_n,
parent=self)
rows = []
for n, full_filename in enumerate(filenames):
if progressbar.wasCanceled():
break
self.currDir = os.path.dirname(full_filename)
try:
newTrace = TraceContainer(filename=full_filename,
loaded_from_ascii=True)
except AttributeError: # if a non-trace file was selected
warnings.warn(
f"This file could not be read: \n{full_filename}",
UserWarning,
)
continue
if (n % update_every_n) == 0:
progressbar.increment()
# If file wasn't loaded properly, skip
if newTrace.load_successful is False:
continue
# Don't load duplicates
if newTrace.name in self.data.traces.keys():
continue
self.data.traces[newTrace.name] = newTrace
item = QStandardItem(newTrace.name)
rows.append(item)
# Don't touch the GUI until loading is done
[self.listModel.appendRow(row) for row in rows]
[
self.listModel.item(i).setCheckable(True)
for i in range(self.listModel.rowCount())
]
self.listView.repaint()
progressbar.close()
if select_top_row:
self.selectListViewTopRow()
self.getCurrentListObject()
self.setConfig(gvars.key_lastOpenedDir, self.currDir)
def test_save_to_right_path(self):
filename = "../resources/traces/Trace.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.tracename = self.file_name
trace.export_trace_to_txt(dir_to_join=self.file_dir)
self.assertTrue(os.path.exists(self.file_path))
def test_reducing_trace_calculating_fret(self):
self.addCleanup(os.remove, self.file_path)
filename = "../resources/traces/Trace.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
trace.red.int[:] = None
trace.red.bg[:] = None
trace.stoi[:] = None
df = trace.get_export_df()
trace.fret[:] = None
trace.tracename = self.file_name
trace.export_trace_to_txt(dir_to_join=self.file_dir,
keep_nan_columns=False)
trace2 = TraceContainer(self.file_path, loaded_from_ascii=True)
self.assertTrue(trace2.load_successful)
df2 = trace2.get_export_df()
np.testing.assert_array_almost_equal(df["E"], df2["E"])
def test_loading_nonALEX_iSMS_trace(self):
filename = "../resources/traces/iSMSNoALEX.txt"
trace = TraceContainer(filename, loaded_from_ascii=True)
self.assertTrue(trace.load_successful)