Merge pull request #31 from scipion-em/devel

send devel to pypi

pyseg/__init__.py

@@ -1,8 +1,9 @@
+# -*- coding: utf-8 -*-
 # **************************************************************************
 # *
-# * Authors:     you (you@yourinstitution.email)
+# * Authors:     Scipion Team
 # *
-# * your institution
+# * National Center of Biotechnology, CSIC, Spain
 # *
 # * 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
@@ -96,8 +97,8 @@ def defineBinaries(cls, env):
     @classmethod
     def _genCmdToGetPySegSrcCode(cls, pySegDir):
         installationCmd = 'wget ' + PYSEG_SOURCE_URL
-        installationCmd += ' && tar zxf %s' % join(pySegDir, basename(PYSEG_SOURCE_URL))
-        installationCmd += ' && rm -rf %s' % join(pySegDir, DEFAULT_VERSION + '.tar')  # rm downloaded file (>600 MB)
+        installationCmd += ' && unzip %s' % join(pySegDir, basename(PYSEG_SOURCE_URL))
+        installationCmd += ' && rm -rf %s' % join(pySegDir, DEFAULT_VERSION + '.zip')  # rm downloaded file (>600 MB)
 
         return installationCmd
 
@@ -131,7 +132,7 @@ def _genCmdToDefineSegCondaEnv(cls):
         installationCmd = cls.getCondaActivationCmd()
 
         # Create the environment
-        installationCmd += 'conda create -y -n %s  -c conda-forge -c anaconda python=2.7 ' \
+        installationCmd += 'conda create -y -n %s  -c conda-forge -c anaconda python=3.6 ' \
                            'opencv=4.2.0 ' \
                            'graph-tool=2.29 && ' % PYSEG_ENV_NAME
 
@@ -147,7 +148,10 @@ def _genCmdToDefineSegCondaEnv(cls):
         installationCmd += 'pip install scikit-learn==0.20.4 && '
         installationCmd += 'pip install scikit-fmm==2021.2.2 && '
         installationCmd += 'pip install scipy==1.2.1 && '
-        installationCmd += 'pip install vtk==8.1.2'
+        installationCmd += 'pip install vtk==8.1.2 '
+        installationCmd += 'pip install astropy==4.1 '
+        installationCmd += 'pip install imageio==2.9.0 '
+        installationCmd += 'pip install future'
 
         return installationCmd
 

pyseg/constants.py

@@ -1,9 +1,9 @@
 # -*- coding: utf-8 -*-
 # **************************************************************************
 # *
-# * Authors:     you (you@yourinstitution.email)
+# * Authors:     Scipion Team
 # *
-# * your institution
+# * National Center of Biotechnology, CSIC, Spain
 # *
 # * 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
@@ -21,15 +21,17 @@
 # * 02111-1307  USA
 # *
 # *  All comments concerning this program package may be sent to the
-# *  e-mail address 'you@yourinstitution.email'
+# *  e-mail address 'scipion@cnb.csic.es'
 # *
 # **************************************************************************
 from os.path import join
 
 PYSEG = 'pySeg'
 PYSEG_HOME = 'PYSEG_HOME'
-DEFAULT_VERSION = '1.1.0'
-PYSEG_SOURCE_URL = 'https://github.com/anmartinezs/pyseg_system/archive/refs/tags/v%s.tar.gz' % DEFAULT_VERSION
+# DEFAULT_VERSION = '1.1.0'
+# PYSEG_SOURCE_URL = 'https://github.com/anmartinezs/pyseg_system/archive/refs/tags/v%s.tar.gz' % DEFAULT_VERSION
+DEFAULT_VERSION = 'jj_py3'
+PYSEG_SOURCE_URL = 'https://github.com/anmartinezs/pyseg_system/archive/refs/heads/%s.zip' % DEFAULT_VERSION
 
 PYSEG_ENV_NAME = 'pySeg-%s' % DEFAULT_VERSION
 PYSEG_ENV_ACTIVATION = 'PYSEG_ENV_ACTIVATION'
@@ -38,24 +40,27 @@
 # Required files location in pyseg-system
 PYSEG_SYSTEM_MAIN = 'pyseg_system-%s' % DEFAULT_VERSION
 DATA_TUTORIALS = join(PYSEG_SYSTEM_MAIN, 'data', 'tutorials')
+FILS_XML_FILES_PATH = join(DATA_TUTORIALS, 'synth_sumb', 'fils', 'in')
 CODE_TUTORIALS = join(PYSEG_SYSTEM_MAIN, 'code', 'tutorials')
 EXP_SOMB = join(CODE_TUTORIALS, 'exp_somb')
-SYNTH_SUMB = join(DATA_TUTORIALS, 'synth_sumb')
+SYNTH_SUMB = join(CODE_TUTORIALS, 'synth_sumb')
 
 PRESEG_SCRIPT = join(EXP_SOMB, 'pre_tomos_seg.py')
 GRAPHS_SCRIPT = join(SYNTH_SUMB, 'tracing', 'mb_graph_mp.py')
 FILS_SCRIPT = join(SYNTH_SUMB, 'tracing', 'mb_fils_network.py')
-FILS_SOURCES = join(SYNTH_SUMB, 'fils', 'in', 'mb_sources.xml')
-FILS_TARGETS = join(SYNTH_SUMB, 'fils', 'in', 'no_mb_targets.xml')
+FILS_SOURCES = join(FILS_XML_FILES_PATH, 'mb_sources.xml')
+FILS_TARGETS = join(FILS_XML_FILES_PATH, 'no_mb_targets.xml')
 PICKING_SCRIPT = join(EXP_SOMB, 'mbo_picking.py')
 PICKING_SLICES = join(DATA_TUTORIALS, 'exp_somb', 'mb_ext.xml')
 POST_REC_SCRIPT = join(SYNTH_SUMB, 'rln', 'post_rec_particles.py')
+PLANE_ALIGN_CLASS_SCRIPT = join(SYNTH_SUMB, 'class', 'plane_align_class.py')
 
 # Generated data
 GRAPHS_OUT = 'graphs'
 FILS_OUT = 'fils'
 PICKING_OUT = 'picking'
 POST_REC_OUT = 'subtomos_post_rec'
+PLANE_ALIGN_CLASS_OUT = 'plane_align_classification'
 
 # Third parties software
 CFITSIO = 'cfitsio'

pyseg/convert.py

@@ -36,6 +36,7 @@
 from relion.convert import Table
 from reliontomo.convert.convert30_tomo import TOMO_NAME, SUBTOMO_NAME, COORD_X, COORD_Y, COORD_Z, ROT, TILT, PSI, \
     RELION_TOMO_LABELS, TILT_PRIOR, PSI_PRIOR, CTF_MISSING_WEDGE, SHIFTX, SHIFTY, SHIFTZ
+from tomo.constants import BOTTOM_LEFT_CORNER
 from tomo.objects import SubTomogram, Coordinate3D, TomoAcquisition, Tomogram
 
 FILE_NOT_FOUND = 'file_not_found'
@@ -57,7 +58,7 @@
 PYSEG_PICKING_STAR = 1
 
 
-def readStarFile(prot, outputSetObject, fileType, starFile=None, invert=True):
+def readStarFile(prot, outputSetObject, fileType, starFile=None, invert=True, returnTable=False):
     warningMsg = None
     # Star file can be provided by the user or not, depending on the protocol invoking this method
     if not starFile:
@@ -88,7 +89,10 @@ def readStarFile(prot, outputSetObject, fileType, starFile=None, invert=True):
                      'values will be considered as 0.' \
                      % '  '.join(['*' + colName + '*' for colName in missingCols])
 
-    return warningMsg
+    if returnTable:
+        return warningMsg, tomoTable
+    else:
+        return warningMsg
 
 
 def manageIhDims(fileName, z, n):
@@ -132,9 +136,9 @@ def _relionTomoStar2Subtomograms(prot, outputSubTomogramsSet, tomoTable, starPat
         tiltPrior = row.get(TILT_PRIOR, 0)
         psiPrior = row.get(PSI_PRIOR, 0)
         ctf3d = row.get(CTF_MISSING_WEDGE, FILE_NOT_FOUND)
-        coordinate3d.setX(float(x))
-        coordinate3d.setY(float(y))
-        coordinate3d.setZ(float(z))
+        coordinate3d.setX(float(x), BOTTOM_LEFT_CORNER)
+        coordinate3d.setY(float(y), BOTTOM_LEFT_CORNER)
+        coordinate3d.setZ(float(z), BOTTOM_LEFT_CORNER)
         coordinate3d._3dcftMrcFile = String(join(starPath, ctf3d))  # Used for the ctf3d generation in Relion
         M = _getTransformMatrix(row, invert)
         transform.setMatrix(M)
@@ -236,19 +240,20 @@ def getTomoSetFromStar(prot, starFile):
 def _pysegStar2Coords3D(prot, output3DCoordSet, tomoTable, invert):
     for tomoNum, tomo in enumerate(prot.tomoSet.iterItems()):
         tomoName = tomo.getFileName().replace(':mrc', '')
-        for ancestorName, row in zip(prot.tomoList, tomoTable):
-            if ancestorName == tomoName:
+        for row in tomoTable:
+            # Create the set of coordinates referring each of them to its corresponding tomogram (ancestor)
+            if row.get(TOMO_NAME) == tomoName:
                 coordinate3d = Coordinate3D()
                 coordinate3d.setVolId(tomoNum)
+                coordinate3d.setVolume(tomo)
                 x = row.get(COORD_X, 0)
                 y = row.get(COORD_Y, 0)
                 z = row.get(COORD_Z, 0)
                 M = _getTransformMatrix(row, invert)
-                coordinate3d.setX(float(x))
-                coordinate3d.setY(float(y))
-                coordinate3d.setZ(float(z))
+                coordinate3d.setX(float(x), BOTTOM_LEFT_CORNER)
+                coordinate3d.setY(float(y), BOTTOM_LEFT_CORNER)
+                coordinate3d.setZ(float(z), BOTTOM_LEFT_CORNER)
                 coordinate3d.setMatrix(M)
-                coordinate3d.setVolume(tomo)
                 coordinate3d._pysegMembrane = String(row.get(SUBTOMO_NAME, FILE_NOT_FOUND))
 
                 # Add current subtomogram to the output set

pyseg/protocols.conf

@@ -12,5 +12,9 @@ Tomography = [
             {"tag": "protocol", "value": "ProtPySegGFP", "text": "pyseg - graphs, fils and picking"},
             {"tag": "protocol", "value": "ProtPySegPostRecParticles", "text": "pyseg - post rec particles"}
         ]}
-	]}
+	]},
+    {"tag": "section", "text": "Subtomogram averaging", "icon": "bookmark.png", "children": [
+        {"tag": "protocol", "value": "ProtPySegPostRecParticles", "text": "pyseg - post rec particles"},
+        {"tag": "protocol", "value": "ProtPySegPlaneAlignClassification", "text": "pyseg - 2d classification"}
+    ]}
  ]

pyseg/protocols/__init__.py

@@ -30,3 +30,4 @@
 from .protocol_fils import ProtPySegFils
 from .protocol_picking import ProtPySegPicking
 from .protocol_pre_seg import ProtPySegPreSegParticles
+from .protocol_2d_classification import ProtPySegPlaneAlignClassification