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import os
import pytest
import numpy as np
raw_path = os.path.abspath(os.path.join('.', __file__, '..', '..'))
if raw_path not in os.sys.path:
os.sys.path.append(raw_path)
import bioxtasraw.RAWAPI as raw
@pytest.fixture()
def new_settings():
settings = raw.load_settings(os.path.join('.', 'data', 'settings_new.cfg'))
return settings
def test_save_settings(new_settings, temp_directory):
raw.save_settings(new_settings, 'test_settings.cfg', temp_directory)
with open(os.path.join(temp_directory, 'test_settings.cfg'), 'r') as f:
test_settings = f.read()
with open(os.path.join('.', 'data', 'settings_new.cfg'), 'r') as f:
exp_settings = f.read()
exclude_keys = ['ATSASDir']
test_settings = test_settings.split('\n')
for line in test_settings:
for key in exclude_keys:
if key in line:
test_settings.remove(line)
test_settings='\n'.join(test_settings)
exp_settings = exp_settings.split('\n')
for line in exp_settings:
for key in exclude_keys:
if key in line:
exp_settings.remove(line)
exp_settings='\n'.join(exp_settings)
assert test_settings == exp_settings
def test_save_profile(gi_sub_profile, temp_directory):
raw.save_profile(gi_sub_profile, 'test_profile.dat', temp_directory)
with open(os.path.join(temp_directory, 'test_profile.dat'), 'r') as f:
test_profile = f.read()
with open(os.path.join('.', 'data', 'glucose_isomerase.dat'), 'r') as f:
exp_profile = f.read()
exclude_keys = ['filename']
test_profile = test_profile.split('\n')
for line in test_profile:
for key in exclude_keys:
if key in line:
test_profile.remove(line)
test_profile='\n'.join(test_profile)
exp_profile = exp_profile.split('\n')
for line in exp_profile:
for key in exclude_keys:
if key in line:
exp_profile.remove(line)
exp_profile='\n'.join(exp_profile)
assert test_profile == exp_profile
def test_save_profile_sans(sans_profile, temp_directory):
raw.save_profile(sans_profile, 'test_sans_profile.dat', temp_directory)
with open(os.path.join(temp_directory, 'test_sans_profile.dat'), 'r') as f:
test_profile = f.read()
with open(os.path.join('.', 'data', 'sans_data.dat'), 'r') as f:
exp_profile = f.read()
exclude_keys = ['filename']
test_profile = test_profile.split('\n')
for line in test_profile:
for key in exclude_keys:
if key in line:
test_profile.remove(line)
test_profile='\n'.join(test_profile)
exp_profile = exp_profile.split('\n')
for line in exp_profile:
for key in exclude_keys:
if key in line:
exp_profile.remove(line)
exp_profile='\n'.join(exp_profile)
assert test_profile == exp_profile
def test_save_gnom_ift(gi_gnom_ift, temp_directory):
raw.save_ift(gi_gnom_ift, 'test_gnom_ift.out', temp_directory)
with open(os.path.join(temp_directory, 'test_gnom_ift.out'), 'r') as f:
test_ift = f.read()
with open(os.path.join('.', 'data', 'glucose_isomerase.out'), 'r') as f:
exp_ift = f.read()
assert test_ift == exp_ift
def test_save_bift_ift(gi_bift_ift, temp_directory):
raw.save_ift(gi_bift_ift, 'test_bift_ift.ift', temp_directory)
with open(os.path.join(temp_directory, 'test_bift_ift.ift'), 'r') as f:
test_ift = f.read()
with open(os.path.join('.', 'data', 'glucose_isomerase.ift'), 'r') as f:
exp_ift = f.read()
exclude_keys = ['filename']
test_ift = test_ift.split('\n')
for line in test_ift:
for key in exclude_keys:
if key in line:
test_ift.remove(line)
test_ift='\n'.join(test_ift)
exp_ift = exp_ift.split('\n')
for line in exp_ift:
for key in exclude_keys:
if key in line:
exp_ift.remove(line)
exp_ift='\n'.join(exp_ift)
assert test_ift == exp_ift
def test_save_series_dats(series_dats, temp_directory):
raw.save_series(series_dats, 'test_series_dats.hdf5', temp_directory)
test_series = raw.load_series([os.path.join(temp_directory,
'test_series_dats.hdf5')])[0]
assert test_series._file_list == series_dats._file_list
assert all(test_series.total_i == series_dats.total_i)
assert test_series.window_size == series_dats.window_size
assert test_series.buffer_range == series_dats.buffer_range
assert test_series.buffer_range == series_dats.buffer_range
assert test_series.sample_range == series_dats.sample_range
assert test_series.sample_range == series_dats.sample_range
assert test_series.baseline_start_range == series_dats.baseline_start_range
assert test_series.baseline_end_range == series_dats.baseline_end_range
assert all(test_series.rg_list == series_dats.rg_list)
assert all(test_series.rger_list == series_dats.rger_list)
assert all(test_series.i0_list == series_dats.i0_list)
assert all(test_series.i0er_list == series_dats.i0er_list)
assert all(test_series.vpmw_list == series_dats.vpmw_list)
assert all(test_series.vcmw_list == series_dats.vcmw_list)
assert all(test_series.vcmwer_list == series_dats.vcmwer_list)
assert test_series.series_type == series_dats.series_type
assert test_series._scale_factor == series_dats._scale_factor
assert test_series._offset_value == series_dats._offset_value
assert test_series._frame_scale_factor == series_dats._frame_scale_factor
assert test_series.mol_type == series_dats.mol_type
assert test_series.mol_density == series_dats.mol_density
assert test_series.already_subtracted == series_dats.already_subtracted
assert len(test_series.subtracted_sasm_list) == len(series_dats.subtracted_sasm_list)
assert len(test_series.use_subtracted_sasm) == len(series_dats.use_subtracted_sasm)
assert all(test_series.total_i_sub == series_dats.total_i_sub)
assert test_series.baseline_type == series_dats.baseline_type
assert len(test_series.baseline_subtracted_sasm_list) == len(series_dats.baseline_subtracted_sasm_list)
assert len(test_series.use_baseline_subtracted_sasm) == len(series_dats.use_baseline_subtracted_sasm)
assert all(test_series.total_i_bcsub == series_dats.total_i_bcsub)
def test_save_series_images(series_images, temp_directory):
raw.save_series(series_images, 'test_series_images.hdf5', temp_directory)
test_series = raw.load_series([os.path.join(temp_directory,
'test_series_images.hdf5')])[0]
assert test_series._file_list == series_images._file_list
assert all(test_series.total_i == series_images.total_i)
assert test_series.window_size == series_images.window_size
assert test_series.buffer_range == series_images.buffer_range
assert test_series.buffer_range == series_images.buffer_range
assert test_series.sample_range == series_images.sample_range
assert test_series.sample_range == series_images.sample_range
assert test_series.baseline_start_range == series_images.baseline_start_range
assert test_series.baseline_end_range == series_images.baseline_end_range
assert all(test_series.rg_list == series_images.rg_list)
assert all(test_series.rger_list == series_images.rger_list)
assert all(test_series.i0_list == series_images.i0_list)
assert all(test_series.i0er_list == series_images.i0er_list)
assert all(test_series.vpmw_list == series_images.vpmw_list)
assert all(test_series.vcmw_list == series_images.vcmw_list)
assert all(test_series.vcmwer_list == series_images.vcmwer_list)
assert test_series.series_type == series_images.series_type
assert test_series._scale_factor == series_images._scale_factor
assert test_series._offset_value == series_images._offset_value
assert test_series._frame_scale_factor == series_images._frame_scale_factor
assert test_series.mol_type == series_images.mol_type
assert test_series.mol_density == series_images.mol_density
assert test_series.already_subtracted == series_images.already_subtracted
assert len(test_series.subtracted_sasm_list) == len(series_images.subtracted_sasm_list)
assert len(test_series.use_subtracted_sasm) == len(series_images.use_subtracted_sasm)
assert all(test_series.total_i_sub == series_images.total_i_sub)
assert test_series.baseline_type == series_images.baseline_type
assert len(test_series.baseline_subtracted_sasm_list) == len(series_images.baseline_subtracted_sasm_list)
assert len(test_series.use_baseline_subtracted_sasm) == len(series_images.use_baseline_subtracted_sasm)
assert all(test_series.total_i_bcsub == series_images.total_i_bcsub)
def test_save_series_sasbdb_keywords(series_sasbdb_keywords, temp_directory):
raw.save_series(series_sasbdb_keywords, 'test_series_sasbdb_keywords.hdf5', temp_directory)
test_series = raw.load_series([os.path.join(temp_directory,
'test_series_sasbdb_keywords.hdf5')])[0]
assert test_series._file_list == series_sasbdb_keywords._file_list
assert all(test_series.total_i == series_sasbdb_keywords.total_i)
assert test_series.window_size == series_sasbdb_keywords.window_size
assert test_series.buffer_range == series_sasbdb_keywords.buffer_range
assert test_series.buffer_range == series_sasbdb_keywords.buffer_range
assert test_series.sample_range == series_sasbdb_keywords.sample_range
assert test_series.sample_range == series_sasbdb_keywords.sample_range
assert test_series.baseline_start_range == series_sasbdb_keywords.baseline_start_range
assert test_series.baseline_end_range == series_sasbdb_keywords.baseline_end_range
assert all(test_series.rg_list == series_sasbdb_keywords.rg_list)
assert all(test_series.rger_list == series_sasbdb_keywords.rger_list)
assert all(test_series.i0_list == series_sasbdb_keywords.i0_list)
assert all(test_series.i0er_list == series_sasbdb_keywords.i0er_list)
assert all(test_series.vpmw_list == series_sasbdb_keywords.vpmw_list)
assert all(test_series.vcmw_list == series_sasbdb_keywords.vcmw_list)
assert all(test_series.vcmwer_list == series_sasbdb_keywords.vcmwer_list)
assert test_series.series_type == series_sasbdb_keywords.series_type
assert test_series._scale_factor == series_sasbdb_keywords._scale_factor
assert test_series._offset_value == series_sasbdb_keywords._offset_value
assert test_series._frame_scale_factor == series_sasbdb_keywords._frame_scale_factor
assert test_series.mol_type == series_sasbdb_keywords.mol_type
assert test_series.mol_density == series_sasbdb_keywords.mol_density
assert test_series.already_subtracted == series_sasbdb_keywords.already_subtracted
assert len(test_series.subtracted_sasm_list) == len(series_sasbdb_keywords.subtracted_sasm_list)
assert len(test_series.use_subtracted_sasm) == len(series_sasbdb_keywords.use_subtracted_sasm)
assert all(test_series.total_i_sub == series_sasbdb_keywords.total_i_sub)
assert test_series.baseline_type == series_sasbdb_keywords.baseline_type
assert len(test_series.baseline_subtracted_sasm_list) == len(series_sasbdb_keywords.baseline_subtracted_sasm_list)
assert len(test_series.use_baseline_subtracted_sasm) == len(series_sasbdb_keywords.use_baseline_subtracted_sasm)
assert all(test_series.total_i_bcsub == series_sasbdb_keywords.total_i_bcsub)
def test_save_report_all(gi_sub_profile, gi_gnom_ift, bsa_series, temp_directory):
raw.save_report('test_all.pdf', temp_directory, [gi_sub_profile], [gi_gnom_ift],
[bsa_series])
assert os.path.exists(os.path.join(temp_directory, 'test_all.pdf'))
def test_save_report_prof(gi_sub_profile, temp_directory):
raw.save_report('test_prof.pdf', temp_directory, [gi_sub_profile])
assert os.path.exists(os.path.join(temp_directory, 'test_prof.pdf'))
def test_save_report_ift(gi_gnom_ift, temp_directory):
raw.save_report('test_ift.pdf', temp_directory, ifts=[gi_gnom_ift])
assert os.path.exists(os.path.join(temp_directory, 'test_ift.pdf'))
def test_save_report_series(bsa_series, temp_directory):
raw.save_report('test_series.pdf', temp_directory, series=[bsa_series])
assert os.path.exists(os.path.join(temp_directory, 'test_series.pdf'))
def test_save_report_series_with_efa(bsa_series, temp_directory):
efa_profiles, converged, conv_data, rotation_data = raw.efa(bsa_series,
[[130, 187], [149, 230]], framei=130, framef=230)
raw.save_report('test_series_efa.pdf', temp_directory, series=[bsa_series])
assert os.path.exists(os.path.join(temp_directory, 'test_series_efa.pdf'))
def test_save_report_series_with_regals(bsa_series, temp_directory):
prof1_settings = {
'type' : 'simple',
'lambda' : 0.0,
'auto_lambda' : False,
'kwargs' : {},
}
conc1_settings = {
'type' : 'smooth',
'lambda' : 6.0e3,
'auto_lambda' : False,
'kwargs' : {
'xmin' : 130,
'xmax' : 187,
'Nw' : 50,
'is_zero_at_xmin' : False,
'is_zero_at_xmax' : True,
}
}
prof2_settings = {
'type' : 'simple',
'lambda' : 0.0,
'auto_lambda' : False,
'kwargs' : {},
}
conc2_settings = {
'type' : 'smooth',
'lambda' : 8.0e3,
'auto_lambda' : False,
'kwargs' : {
'xmin' : 149,
'xmax' : 230,
'Nw' : 50,
'is_zero_at_xmin' : True,
'is_zero_at_xmax' : False,
}
}
comp_settings = [(prof1_settings, conc1_settings),
(prof2_settings, conc2_settings)]
regals_profiles, regals_ifts, conc, reg_conc, mixture, params, residual = raw.regals(bsa_series,
comp_settings, framei=130, framef=230)
raw.save_report('test_series_regals.pdf', temp_directory, series=[bsa_series])
assert os.path.exists(os.path.join(temp_directory, 'test_series_regals.pdf'))
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