def test_get_sample_gate_events(self):
wsp_path = "examples/data/8_color_data_set/8_color_ICS_simple.wsp"
sample_grp = 'DEN'
sample_id = '101_DEN084Y5_15_E01_008_clean.fcs'
gate_name = 'CD3+'
fks = Session(copy.deepcopy(test_samples_8c_full_set))
fks.import_flowjo_workspace(wsp_path, ignore_missing_files=True)
fks.analyze_samples(sample_grp, sample_id)
sample_comp = fks.get_sample_comp_matrices(sample_grp, sample_id)[0]
sample_xform = transforms.LogicleTransform('my_logicle',
param_t=262144.0,
param_w=1.0,
param_m=4.418539922,
param_a=0.0)
df_gated_events = fks.get_gate_events(sample_grp,
sample_id,
gate_name,
matrix=sample_comp,
transform=sample_xform)
self.assertIsInstance(df_gated_events, pd.DataFrame)
self.assertEqual(len(df_gated_events), 133670)
def test_transform_sample_logical(self):
xform = transforms.LogicleTransform('logicle',
param_t=10000,
param_w=0.5,
param_m=4.5,
param_a=0)
data1_sample.apply_transform(xform)
self.assertIsInstance(data1_sample._transformed_events, np.ndarray)
def test_inverse_logicle_transform():
xform = transforms.LogicleTransform('logicle',
param_t=10000,
param_w=0.5,
param_m=4.5,
param_a=0)
y = xform.apply(test_data_range1)
x = xform.inverse(y)
np.testing.assert_array_almost_equal(test_data_range1, x, decimal=10)
import sys
import os
from pathlib import Path
import numpy as np
import pandas as pd
sys.path.append(os.path.abspath('..'))
from flowkit import Sample, transforms
data1_fcs_path = 'examples/gate_ref/data1.fcs'
data1_sample = Sample(data1_fcs_path)
xform_logicle = transforms.LogicleTransform('logicle',
param_t=10000,
param_w=0.5,
param_m=4.5,
param_a=0)
class LoadSampleTestCase(unittest.TestCase):
"""Tests for loading FCS files as Sample objects"""
def test_load_from_fcs_file_path(self):
"""Test creating Sample object from an FCS file path"""
fcs_file_path = "examples/test_data_2d_01.fcs"
sample = Sample(fcs_path_or_data=fcs_file_path)
self.assertIsInstance(sample, Sample)
def test_load_from_pathlib(self):
