Source code for sphire.constants

# -*- coding: utf-8 -*
# **************************************************************************
# *
# * Authors:    Peter Horvath [1]
# *             Pablo Conesa  [1]
# *             J.M. De la Rosa Trevin (delarosatrevin@scilifelab.se) [2]
# *             Jorge Jiménez [1]
# *
# *
# * [1] Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# * [2] SciLifeLab, Stockholm University
# *
# * 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 'scipion@cnb.csic.es'
# *
# **************************************************************************

import os


# crYOLO ###############################################################################################################

[docs]def getCryoloEnvName(version, useCpu=False): return "cryolo%s-%s" % ('CPU' if useCpu else '', version)
V1_5_4 = "1.5.4" V1_6_1 = "1.6.1" V1_7_2 = "1.7.2" V1_7_6 = "1.7.6" VERSIONS = [V1_5_4, V1_6_1, V1_7_2, V1_7_6] CRYOLO_DEFAULT_VER_NUM = V1_7_6 DEFAULT_ENV_NAME = getCryoloEnvName(CRYOLO_DEFAULT_VER_NUM) DEFAULT_ACTIVATION_CMD = 'conda activate ' + DEFAULT_ENV_NAME CRYOLO_ENV_ACTIVATION = 'CRYOLO_ENV_ACTIVATION' DEFAULT_ENV_NAME_CPU = getCryoloEnvName(CRYOLO_DEFAULT_VER_NUM, useCpu=True) DEFAULT_ACTIVATION_CMD_CPU = 'conda activate ' + DEFAULT_ENV_NAME_CPU CRYOLO_ENV_ACTIVATION_CPU = 'CRYOLO_ENV_ACTIVATION_CPU' CRYOLO_CUDA_LIB = 'CRYOLO_CUDA_LIB' # Model constants def _modelFn(modelKey): return 'gmodel_phosnet_%s.h5' % modelKey CRYOLO_GENMOD_VAR = 'CRYOLO_GENERIC_MODEL' CRYOLO_GENMOD_NN_VAR = 'CRYOLO_GENERIC_DENOISED_MODEL' CRYOLO_GENMOD = 'cryolo_model' CRYOLO_GENMOD_201909 = '201909' CRYOLO_GENMOD_201909_FN = _modelFn(CRYOLO_GENMOD_201909) CRYOLO_GENMOD_201910 = '201910' CRYOLO_GENMOD_201910_FN = _modelFn(CRYOLO_GENMOD_201910) CRYOLO_GENMOD_202002 = '202002_N63' CRYOLO_GENMOD_202002_FN = _modelFn(CRYOLO_GENMOD_202002) CRYOLO_GENMOD_202005 = '202005_N63_c17' CRYOLO_GENMOD_202005_FN = _modelFn(CRYOLO_GENMOD_202005) CRYOLO_GENMOD_NN_202005 = '202005_nn_N63_c17' CRYOLO_GENMOD_NN_202005_FN = _modelFn(CRYOLO_GENMOD_NN_202005) # Default model (latest usually) CRYOLO_GENMOD_DEFAULT = os.path.join(CRYOLO_GENMOD + "-" + CRYOLO_GENMOD_202005, CRYOLO_GENMOD_202005_FN) CRYOLO_GENMOD_NN_DEFAULT = os.path.join(CRYOLO_GENMOD + "-" + CRYOLO_GENMOD_NN_202005, CRYOLO_GENMOD_NN_202005_FN) # crYOLO supported input formats for micrographs CRYOLO_SUPPORTED_FORMATS = [".mrc", ".tif", ".tiff", ".jpg"] # Input options for the training model INPUT_MODEL_GENERAL = 0 INPUT_MODEL_GENERAL_DENOISED = 1 INPUT_MODEL_OTHER = 2 INPUT_MODEL_GENERAL_NS = 3 # crYOLO - NEGATIVE STAIN ############################################################################################## def _negStainModelFn(modelKey): return 'gmodel_phosnet_negstain_{}.h5'.format(modelKey) CRYOLO_NS_GENMOD_VAR = 'CRYOLO_NS_GENERIC_MODEL' CRYOLO_NS_GENMOD = 'cryolo_negstain_model' CRYOLO_NS_GENMOD_20190226 = '20190226' CRYOLO_NS_GENMOD_20190226_FN = _negStainModelFn(CRYOLO_NS_GENMOD_20190226) CRYOLO_NS_GENMOD_DEFAULT = os.path.join(CRYOLO_NS_GENMOD + "-" + CRYOLO_NS_GENMOD_20190226, CRYOLO_NS_GENMOD_20190226_FN) # JANNI ################################################################################################################ def _janniModelFn(modelKey): return 'gmodel_janni_{}.h5'.format(modelKey) JANNI_GENMOD_VAR = 'JANNI_GENERIC_MODEL' JANNI_GENMOD = "janni_model" # Name JANNI_GENMOD_20190703 = "20190703" # Version JANNI_GENMOD_20190703_FN = _janniModelFn(JANNI_GENMOD_20190703) # File name with extension JANNI_GENMOD_DEFAULT = os.path.join("{}-{}".format(JANNI_GENMOD, JANNI_GENMOD_20190703), JANNI_GENMOD_20190703_FN)