def setData(cls):
cls.dataset = DataSet(name='test_zernike3d',
folder='test_zernike3d',
files={
'particles':
'particles/images_1720_norm.xmd',
'volumes': 'volumes/*.vol',
'1720': 'volumes/EMD-1720_norm.vol',
'1723': 'volumes/EMD-1723_norm.vol'
})
cls.dataset = DataSet.getDataSet('test_zernike3d')
cls.particles = cls.dataset.getFile('particles')
cls.volumes = cls.dataset.getFile('volumes')
cls.volume_1720 = cls.dataset.getFile('1720')
cls.volume_1723 = cls.dataset.getFile('1723')
cls.clnm_pd_cpu_gold = cls.dataset.getFile(
'gold_standard_pd/CPU/Volumes_clnm.txt')
cls.clnm_pd_gpu_gold = cls.dataset.getFile(
'gold_standard_pd/GPU/Volumes_clnm.txt')
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from pyworkflow.tests import DataSet
DataSet(name='reliontomo',
folder='reliontomo',
files={
'refVol': 'caja72_job30_run_it025_class005.mrc',
'mask': 'mascara_cilindro_caja72.mrc',
'tiltseries': '*.mrcs',
'tomograms': '*ali_bin1.mrc',
'tlts': '*.tlt',
'doseFiles': '*.txt',
'dynamoTables': '*.tbl'
})
# * MRC Laboratory of Molecular Biology (MRC-LMB)
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from pyworkflow.tests import DataSet
from .test_protocols_gctf import TestGctf, TestGctfRefine
from .test_protocols_gctf_ts import TestGctfTs
DataSet(name='tutorialDataImodCTF',
folder='tutorialDataImodCTF',
files={'tsCtf1': 'WTI042413_1series4.st'})
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from pyworkflow.tests import DataSet
DataSet(name='tomo-em',
folder='tomo-em',
files={
'tomo': 'tomo_8_mn.mrc',
'etomo': 'tutorialData',
})
from pyworkflow.tests import DataSet
import tests_picking
# Define aitom dataset (hosted at scipion server)
DataSet(name='aitom',
folder='aitom',
files={
'cellular': 'aitom_demo_cellular_tomogram.mrc',
'single_particle': 'aitom_demo_single_particle_tomogram.mrc',
'pickle': 'aitom_demo_subtomograms.pickle'
})
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from pyworkflow.tests import DataSet
DataSet(name='tomo-em',
folder='tomo-em',
files={
'ts1': 'tutorialData/BBa.st',
'ts2': 'tutorialData/BBb.st'
})
DataSet(name='tutorialDataImodCTF',
folder='tutorialDataImodCTF',
files={'tsCtf1': 'WTI042413_1series4.st'})
def setUpClass(cls):
setupTestProject(cls)
cls.dataset = DataSet(folder='tomo-em', name='tomo-em',
files={'empiar': 'EMPIAR-10164'})
cls.getFileM = cls.dataset.getFile('empiar')
from pyworkflow.tests import DataSet
DataSet(name='pyseg',
folder='pyseg',
files={
'presegTomo': 'Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED.mrc',
'presegMask':
'Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED_material.mrc',
'posRecMask': 'cylMaskk40.mrc',
'mbMask': 'mbMask40.mrc',
'subtomosTbl': 'Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED.tbl',
'coordsTbl': 'Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED.tbl',
'posRecCoordsDir': 'posRecCoords',
'coords': 'posRecCoords/*.mrc',
'tiltSeries': 'Pertuzumab_1_defocus_25um_tomo_7_ali.mrc',
'tltFile': 'Pertuzumab_1_defocus_25um_tomo_7_ali.tlt',
'doseFile': 'Pertuzumab_1_defocus_25um_tomo_7_ali_ExpDose.txt'
})
class DSKeys:
ROOT = 'root'
IMPORTPATH = 'importPath'
TILEIMAGE1 = 'tileImage1'
TILEIMAGE2 = 'tileImage2'
TILE1DM = 'tile1dm'
TILEMRC1= 'mrc1'
ATLAS_DIR='atlasdir'
ATLAS_FOLDER = 'GRID_05/ATLAS'
DataSet(name='atlas', folder='atlas',
files={
DSKeys.ROOT: '',
DSKeys.IMPORTPATH: 'GRID_??/DATA/Images-Disc1/GridSquare_*/Data',
DSKeys.ATLAS_DIR: ATLAS_FOLDER,
DSKeys.TILEIMAGE1: os.path.join(ATLAS_FOLDER,'Tile_1818556_1_1.jpg'),
DSKeys.TILEIMAGE2: os.path.join(ATLAS_FOLDER,'Tile_1818512_0_1.jpg'),
DSKeys.TILE1DM: os.path.join(ATLAS_FOLDER,'Tile_1818512_0_1.dm'),
DSKeys.TILEMRC1: os.path.join(ATLAS_FOLDER,'Tile_1818512_0_1.mrc'),
})
class TestAtlas(BaseTest):
""" Test most basic elements """
@classmethod
def setUpClass(cls):
cls.dataset = DataSet.getDataSet('atlas')
setupTestProject(cls)
def test_FEIImporter(self):
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from .test_convert_relion import *
from .test_protocols_relion import *
from .test_protocols_relion3 import *
from .test_workflow_relion3 import *
from pyworkflow.tests import DataSet
DataSet(name='relion31_tutorial_precalculated',
folder='relion31_tutorial_precalculated',
files={})
from pyworkflow.tests import DataSet
DataSet(name='tomo-em',
folder='tomo-em',
files={
'tomo1': 'overview_wbp.em',
'tomo2': 'overview_wbp2.em',
'tomo3': 'tomo_8_mn.mrc',
'subtomo': 'basename.hdf',
'eman_coordinates': 'coordinates3Deman2',
'etomo': 'tutorialData',
'empiar': 'EMPIAR-10164',
'tsMParentFolder': 'ts_tsM_and_mdocs',
'tsM10Dir': 'ts_tsM_and_mdocs/Tomo_10',
'tsM31Dir': 'ts_tsM_and_mdocs/Tomo_31',
'empiarMdocDirOk':
'ts_tsM_and_mdocs/mdocs/realFromEmpiar/complete',
'empiarMdocDirNoOk':
'ts_tsM_and_mdocs/mdocs/realFromEmpiar/incomplete',
'realFileNoVoltage1': 'tomo4_delay.st.mdoc',
'realFileNoVoltage2': 'TS_54.mrc.mdoc',
'simErrorMdocDir':
'ts_tsM_and_mdocs/mdocs/editedForErrorSimulation',
'noMaginficationMdoc': 'NoMagnification.mdoc',
'noSamplingRateMdoc': 'NoPixelSpacing.mdoc',
'noVoltagenoSRateMdoc': 'NoVoltage_NoPixelSpacing.mdoc',
'someMissingAnglesMdoc': 'SomeTiltAnglesMissing_1_7_48.mdoc',
'noDoseMdoc': 'noDose.mdoc'
})
DataSet(name='reliontomo',
from pyworkflow.tests import DataSet
DataSet(name='cryocare', folder='cryocare',
files={
'rec_even_odd_tomos_dir': 'Tomos_EvenOdd_Reconstructed',
'tomo_even': 'Tomos_EvenOdd_Reconstructed/Tomo110_Even_bin6.mrc',
'tomo_odd': 'Tomos_EvenOdd_Reconstructed/Tomo110_Odd_bin6.mrc',
'model_dir': 'Training_Model',
'training_data_dir': 'Training_Data',
'train_data_file': 'Training_Data/train_data.npz',
'validation_data_file': 'Training_Data/val_data.npz',
'training_data_conf_dir': 'Training_Data_Config',
'training_data_conf': 'Training_Data_Config/training_data_config'
})
def defineDatasets():
""" Defines datasets for testing."""
DataSet(name='igbmc_gempicker',
folder='igbmc_gempicker',
files={
'allMics': 'micrographs/*.mrc',
'mic1': 'micrographs/KLH_Dataset_I_Test_0001.mrc',
'mic2': 'micrographs/KLH_Dataset_I_Test_0002.mrc',
'mask1': 'masks/mask_sideview.tif',
'mask2': 'masks/mask_topview.tif',
'templates': 'templates/*.mrc'
})
DataSet(name='xmipp_tutorial',
folder='xmipp_tutorial',
files={
'aligned_particles': 'gold/aligned_particles.sqlite',
'allMics': 'micrographs/*.mrc',
'boxingDir': 'pickingEman/info',
'boxingFile': 'pickingEman/info/BPV_1386_info.json',
'coordsGoldSqlite': 'gold/coordinates_gold.sqlite',
'ctfGold': 'gold/xmipp_ctf.ctfparam',
'ctf': 'ctfs/ctfs.sqlite',
'images10': 'gold/images10.xmd',
'mic1': 'micrographs/BPV_1386.mrc',
'mic2': 'micrographs/BPV_1387.mrc',
'mic3': 'micrographs/BPV_1388.mrc',
'micsGoldSqlite': 'gold/micrographs_gold.sqlite',
'micsGoldSqlite2': 'gold/micrographs2_gold.sqlite',
'micsGoldXmd': 'gold/micrographs_gold.xmd',
'micsSqlite': 'micrographs/micrographs.sqlite',
'particles': 'particles/*.hdf',
'particles1': 'particles/BPV_1386_ptcls.hdf',
'particles2': 'particles/BPV_particles.sqlite',
'particles3': 'particles/BPV_particles_aligned.sqlite',
'posAllDir': 'pickingXmipp/pickedAll',
'posSupervisedDir': 'pickingXmipp/pickedSupervised',
'rctCoords': 'rct/pickingXmipp',
'rctMicsT': 'rct/micrographs/*T.mrc',
'rctMicsU': 'rct/micrographs/*U.mrc',
'vol1': 'volumes/BPV_scale_filtered_windowed_64.vol',
'vol2': 'volumes/volume_1_iter_002.mrc',
'vol3': 'volumes/volume_2_iter_002.mrc',
'vol4': 'volumes/helix_59_4__6_7.vol',
'vol110': 'volumes/BPV_scale_filtered_windowed_110.vol',
'volumes': 'volumes/*.mrc',
'mask2d': 'masks/mask2d.xmp',
'mask3d': 'masks/mask.vol',
'ctfsDir': 'ctfs'
})
DataSet(name='mda',
folder='hemoglobin_mda',
files={
'particles': 'particles/*.spi',
'particlesDir': 'particles',
'volumes': 'volumes/*.spi',
'volumesDir': 'volumes',
'averages': 'averages/averages.stk',
'averagesDir': 'averages'
})
DataSet(name='nma',
folder='nma',
files={
'pdb': 'pdb/AK.pdb',
'vol': 'volumes/AK_LP10.vol',
'particles': 'particles/img.stk'
})
DataSet(name='powerfit',
folder='powerfit',
files={
'pdb': '3j79-pdb-bundle1.pdb',
'vol': 'ribosome_4.vol'
})
DataSet(name='tomo',
folder='xmipp_tomo_test',
files={
'vol1': 'volumes/subvols_6E6.001.mrc.spi',
'vol2': 'volumes/subvols_6E6.002.mrc.spi',
'vol3': 'volumes/subvols_6E6.003.mrc.spi',
'volumes': 'volumes/*.spi'
})
DataSet(name='relion_tutorial',
folder='relion_tutorial',
files={
'allMics': 'micrographs/*.mrc',
'boxingDir': 'pickingEman',
'input_particles': 'gold/input_particles.star',
'particles': 'gold/particles.sqlite',
'posAllDir': 'pickingXmipp',
'relion_it020_data': 'gold/relion_it020_data.star',
'relion_it020_data_newlabels':
'gold/relion_it020_data_newlabels.star',
'volume': 'volumes/reference.mrc',
'import1_data_star':
'import/case1/classify3d_small_it038_data.star',
'import2_data_star': 'import/case2/relion_it015_data.star',
'particles_binary': '006.stk'
})
DataSet(name='relion30_tutorial', folder='relion30_tutorial', files={})
DataSet(name='ribo_movies',
folder='ribo_movies',
files={
'movies': 'movies/1??_*.mrcs',
'posAllDir': 'pickingXmipp',
'volume': 'volumes/reference.mrc'
})
DataSet(name='model',
folder='model',
files={
'classesSelection': 'gold/classes_selection.sqlite',
'modelGoldSqlite': 'gold/model_gold.sqlite',
'modelGoldXml': 'gold/model_gold.xml'
})
DataSet(name='rct',
folder='rct',
files={
'classes': 'classes/classes2D_stable_core.sqlite',
'positions': 'positions',
'tilted': 'micrographs/F_rct_t*.tif',
'untilted': 'micrographs/F_rct_u*.tif'
})
DataSet(name='groel',
folder='groel',
files={
'averages': 'classes/level_classes.stk',
'mic1': 'micrographs/groel-stain.mrc',
'pickingDogpicker': 'pickingDogpicker'
})
# TODO: Files to be deleted after checking no plugin or old scipion
# installations (1.2, ...) are using them:
# reconstRotandShiftFlip_Gold_output.vol (moved to reconstruction/gold)
# reconstRotandShift_Gold_output.vol (moved to reconstruction/gold)
# reconstRotOnly_Gold_output.vol (moved to reconstruction/gold)
DataSet(
name='emx',
folder='emx',
files={
'alignFlip':
'alignment/alignFlip.mrcs',
'alignFlip2':
'alignment/alignFlip2.mrcs',
'alignShiftRotExp':
'alignment/Test1/images.mrc',
'alignShiftRotExpGold':
'alignment/gold/align_shift_rot_exp_gold.mrcs',
'alignReconst':
'alignment/recons.mrcs',
'alignReconstShift':
'alignment/recons_sh.mrcs',
'alignRotOnly':
'alignment/align_rot_only.mrcs',
'alignRotOnlyGold':
'alignment/gold/align_rot_only_gold.mrcs',
# TODO: transform geometry not working in stacks of volumes
'alignRotOnly3D':
'alignment/align_rot_only_3d.mrcs',
# 'alignRotShift': 'alignment/align_rot_shift.mrcs',
'alignShiftOnly':
'alignment/align_shift_only.mrcs',
'alignShiftOnlyGold':
'alignment/gold/align_shift_only_gold.mrcs',
# TODO: transform geometry not working in stacks of volumes
'alignShiftOnly3D':
'alignment/align_shift_only_3d.mrcs',
'alignShiftRot':
'alignment/align_shift_rot.mrcs',
'alignShiftRotGold':
'alignment/gold/align_shift_rot_gold.mrcs',
# TODO: transform geometry not working in stacks of volumes
'alignShiftRot3D':
'alignment/align_shift_rot_3d.mrcs',
'coordinatesGoldT1':
'coordinates/Test1/coordinates_gold.sqlite',
'coordinatesT1':
'coordinates/Test1/coordinates.emx',
'defocusParticleT2':
'defocusParticle/particles.emx',
'emxMicrographCtf1':
'MicrographsCTF/ctfindCTFEstimation.emx',
'emxMicrographCtf1Gold':
'MicrographsCTF/ctfindCTFEstimation.sqlite',
'micrographsGoldT2':
'defocusParticle/micrographs_gold.sqlite',
'particlesGoldT2':
'defocusParticle/particles_gold.sqlite',
'reconstRotOnly':
'reconstruction/reconstRotOnly.mrcs',
'reconstRotOnlyGold':
'reconstruction/gold/reconstRotOnly_output.vol',
'reconstRotandShift':
'reconstruction/reconstRotandShift.mrcs',
'reconstRotandShiftGold':
'reconstruction/gold/reconstRotandShift_output.vol',
'reconstRotandShiftFlip':
'reconstruction/reconstRotandShiftFlip.mrcs',
'reconstRotandShiftFlipGold':
'reconstruction/gold/reconstRotandShiftFlip_output.vol',
'reconstRotOnlyGoldRln':
'reconstruction/gold/reconstRotOnly_rln_output.vol',
'reconstRotandShiftGoldRln':
'reconstruction/gold/reconstRotandShift_rln_output.vol',
'reconstRotandShiftFlipGoldRln':
'reconstruction/gold/reconstRotandShiftFlip_rln_output.vol'
})
DataSet(name='CTFDiscrepancy',
folder='CTFDiscrepancy',
files={
'emxMicrographCtf1': 'ctfindCTFEstimation.emx',
'emxMicrographCtf2': 'xmipp3CTFEstimation.emx',
'emxMicrographCtf3': 'xmipp3CTFEstimation2.emx',
'ctfsGold': 'ctfs.sqlite'
})
DataSet(
name='movies',
folder='movies',
files={
'movie1':
'ribo/Falcon_2012_06_12-14_33_35_0_movie.mrcs',
'movie2':
'ribo/Falcon_2012_06_12-16_55_40_0_movie.mrcs',
'movie3':
'ribo/Falcon_2012_06_12-17_26_54_0_movie.mrcs',
'movie4':
'qbeta/qbeta.mrc',
'movie5':
'cct/cct_1.em',
'falcon2012_1':
'Falcon_2012_06_12-16_55_40_0_movie.mrcs',
'mrcGain':
'gain.mrc',
'mrcDark':
'dark.mrc',
'spiGain':
'gain.spi',
'spiDark':
'dark.spi',
'eer':
'FoilHole_29355520_Data_29330528_29330530_20200329_234551_Fractions.mrc.eer'
})
DataSet(name='riboMovies',
folder='riboMovies',
files={
'movie1': '30_movie_gc_window.mrcs',
'movie2': '35_movie_gc_window.mrcs',
'movie3': '130_movie_gc_window.mrcs',
'movie4': '165_movie_gc_window.mrcs',
'movie5': '270_movie_gc_window.mrcs',
'allMovies': '*.mrcs'
})
DataSet(name='jmbFalconMovies',
folder='jmbFalconMovies',
files={
'movie1': 'Falcon_2014_07_16-16_32_43_0.mrcs',
'movie2': 'Falcon_2014_07_16-21_37_37_0.mrcs',
'movie3': 'Falcon_2014_07_16-23_30_50_0.mrcs',
'movie4': 'Falcon_2014_07_17-03_21_57_0.mrcs',
'movie5': 'Falcon_2014_07_17-06_55_56_0.mrcs',
'allMovies': '*.mrcs'
})
DataSet(name='grigorieff',
folder='grigorieff',
files={
'particles_rot_shift': 'particles.sqlite',
'ref_volume': 'ref_volume.vol',
'ctfsDir': 'ctfs'
})
DataSet(name='initial_volume',
folder='initial_volume',
files={
'groel': 'groel_64.stk',
'ribosome': 'ribosomeFrank_64_preprocessed.stk',
'bpv': 'bpv_100.stk'
})
DataSet(name='general',
folder='general',
files={'vol_helix': 'volumes/helix_59_4__6_7.vol'})
DataSet(name='SymVirus',
folder='SymVirus',
files={
'whole_vol_half': 'whole_vol_half.vol',
'large_vol_half_th': 'large_vol_half_th.vol',
'small_vol_half_th': 'small_vol_half_th.vol'
})
DataSet(name='xmipp_programs', folder='xmipp_programs', files={})
DataSet(name='resmap',
folder='resmap',
files={
'betagal': 'betaGal.mrc',
'betagal_half1': 'betaGal_half01.mrc',
'betagal_half2': 'betaGal_half02.mrc',
'betagal_mask': 'betaGal_mask.mrc'
})
DataSet(name='10010',
folder='10010',
files={
'initialVolume': 'initialVolume.vol',
'particles': 'particles.sqlite'
})
DataSet(name='model_building_tutorial',
folder='model_building_tutorial',
files={
'vol1': 'volumes/1ake_4-5A.mrc',
'pdb1': 'PDBs/1ake_start.pdb'
})
DataSet(name='eman',
folder='eman',
files={
'micU': 'mics/ip3r10252011-0005_0-2.hdf',
'micT': 'mics/ip3r10252011-0005_10.hdf',
'volume': '3DmapIP3R1_clip_376apix.mrc',
'coords': 'coords/*.json',
'ctfs': 'ctfs/'
})
DataSet(name='deepConsensusPicking',
folder='deepConsensusPicking',
files={
'allMics': 'micrographs/*.mrc',
'autoPickingCoordinates': 'autoPickingCoordinates'
})
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address '*****@*****.**'
# *
# **************************************************************************
from pyworkflow.tests import DataSet
DataSet(name='tomosegmemtv',
folder='tomosegmemtv',
files={'tomogram': 'emd_1155i.mrc'})
DataSet(
name='pyseg',
folder='pyseg',
files={'presegTomo': 'Pertuzumab_1_defocus_25um_tomo_7_aliSIRT_EED.mrc'})
