Verify installation ¶

Some of these tests run very quick. Their main goal is to validate the behavior of some important classes and functions (in the spirit of unit tests).

Other tests are more focused on the execution of protocols and complete workflows. They usually take more time to execute, and require some input data (which should be downloaded automatically on demand).

In the following sections you will find a brief explanation about the more important tests, and their input data. All of them must be executed from the command line using the specified commands.

Table of Contents

Small tests ¶

Basic tests ¶

Plugins	Core, Xmipp, Relion
	`scipion tests pyworkflowtests.tests.test_object.TestObject`
	`scipion tests pyworkflowtests.tests.test_mappers`
	`scipion tests pwem.tests.data.test_data`
	`scipion tests xmipp3.tests.test_convert_xmipp`
	`scipion tests relion.tests.test_convert_relion`

Spider MDA Workflow ¶

Plugins	Spider
Command	`scipion tests spider.tests.test_workflow_spiderMDA`
Input	Fake dataset of Worm Hemoglobin with 76 images
Time	~50 sec

EMX import ¶

Plugins	emxlib
Command	`scipion tests emxlib.tests.test_protocols_emx.TestEmxBase`
Input	The different data sets used in http://i2pc.cnb.csic.es/emx
Time	~10 sec

CTF Discrepancy ¶

Plugins	Xmipp, Cistem
Command	`scipion tests pwem.tests.workflows.test_workflow_xmipp_ctf_consensus.TestCtfConsensus`
Input	CTF obtained from micrograph of PcV (http://dx.doi.org/doi:10.1073/pnas.1404330111)
Time	~10 sec

Medium tests ¶

Xmipp Workflow ¶

Plugins	Xmipp
Command	`scipion tests pwem.tests.workflows.test_workflow_xmipp`
Input	Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained
Time	~300 sec
CPU	i7-2640M 2.8GHz, 8GB RAM

Mixed Workflow 3D Reconstruction ¶

Plugins	Xmipp, EMAN
Command	`scipion tests pwem.tests.workflows.test_workflow_mixed.TestMixedBPV`
Input	Same data as in Xmipp Workflow. A refined volume generated with Frealign is obtained
Time	~150 sec
CPU	i7-2640M 2.8GHz, 8GB RAM

Mixed Workflow Initial Volume ¶

Plugins	Xmipp, EMAN
Command	`scipion tests pwem.tests.workflows.test_workflow_mixed.TestMixedBPV2`
Input	Same data as in Xmipp Workflow. An initial volume generated with EMAN is obtained
Time	~200 sec
CPU	i7-2640M 2.8GHz, 8GB RAM

Large Tests ¶

[WARNING] The following tests must be run on computers with enough processing power.

Mixed Workflow Relion 2D classification ¶

Plugins	Xmipp, Cistem, EMAN, Relion
Command	`scipion tests pwem.tests.workflows.test_workflow_mixed_large.TestMixedRelionTutorial`
Input	Dataset with 20 micrographs of the Ribosome.
Time	~3h sec
CPU	16 CPUs. Xeon(R) E5540 2.53 GHz, 64 GB RAM

Random Conical Tilt reconstruction ¶

Plugins	Xmipp
Command	`scipion tests pwem.tests.workflows.test_workflow_xmipp_rct`
Input	Dataset with 6 pairs of untilted-tilted micrographs.
Time	~15 min
CPU	4 CPUs. Intel(R) Core(TM) i7-2640M CPU @ 2.80GHz, 8 GB RAM

Procotol Tests ¶

Import different type of objects ¶

Plugins	Scipion
Import micrographs	`scipion tests pwem.tests.protocols.test_protocols_import_micrographs`
Import particles	`scipion tests pwem.tests.protocols.test_protocols_import_particles`
Import volumes	`scipion tests pwem.tests.protocols.test_protocols_import_volumes`
Input	From different datasets
Time	~15 min
CPU	i7-2640M 2.8GHz, 8GB RAM

Processing micrographs ¶

Plugins	Xmipp
preprocess	`scipion tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippPreprocessMicrographs`
ctf estimation	`scipion tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippCTFEstimation`
Extract Particles	`scipion tests xmipp3.tests.test_protocols_xmipp_mics.TestXmippExtractParticles`

Software	Cistem
ctf estimation	`scipion tests cistem.tests.test_protocols_cistem.TestCtffind4`
Input	Dataset xmipp tutorial
Time
CPU	i7-2640M 2.8GHz, 8GB RAM

Preprocessing 2D ¶

Software	Xmipp
Create Mask 2D	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippCreateMask2D`
Apply Mask 2D	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyMask2D`
Filter Particles	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippFilterParticles`

Software	Relion
Preprocess Particles	`scipion tests relion.tests.test_protocols_relion.TestRelionPreprocess`
Input	From different datasets
Time	~400 sec
CPU	i7-2640M 2.8GHz, 8GB RAM

Particles alignment and classification ¶

Software	Xmipp
ML2D	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippML2D`
CL2D	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippCL2D`
CL2D Align	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippProtCL2DAlign`
Apply Alignment	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippApplyAlignment`
Rotational Spectra	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippRotSpectra`
Kerdensom	`scipion tests xmipp3.tests.test_protocols_xmipp_2d.TestXmippKerdensom`

Software	Relion
Classify 2D	`scipion tests relion.tests.test_protocols_relion.TestRelionClassify2D`
Input	Mda dataset
CPU	i7-2640M 2.8GHz, 8GB RAM

Preprocessing 3D ¶

Software	Xmipp
Create Mask 3D	`scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippCreateMask3D`
Apply Mask 3D	`scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippApplyMask3D`
Filter Volumes	`scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippFilterVolumes`
Preprocess Volumes	`scipion tests xmipp3.tests.test_protocols_xmipp_3d.TestXmippPreprocessVolumes`
Input	Same data as in Xmipp Workflow.
Time	~400 sec
CPU	i7-2640M 2.8GHz, 8GB RAM

Initial volume ¶

tests	Significant
Software	Xmipp
Reconstruct significant	`scipion tests pwem.tests.workflows.test_workflow_initialvolume.TestSignificant`
Input	Groel data
Time	~27 min
CPU	4 CPUs on Asimov

Classify 3D ¶

tests	Classify 3D
Software	Relion
Relion Classify 3D	`scipion tests relion.tests.test_protocols_relion.TestRelionClassify3D`
Input	MDA data
Time	~200 sec
CPU	i7-2640M 2.8GHz, 8GB RAM