Merge pull request #86 from scipion-em/devel

Release 3.1.21
scipion-em · Nov 15, 2023 · f94f9b5 · f94f9b5
2 parents f0b01ef + 72abae4
commit f94f9b5
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Showing 5 changed files with 26 additions and 36 deletions.
diff --git a/dynamo/__init__.py b/dynamo/__init__.py
@@ -24,14 +24,14 @@
 # *
 # **************************************************************************
 import os.path
-from os.path import join
+from os.path import join, dirname
 import subprocess
 import pwem
 import pyworkflow
 import pyworkflow.utils as pwutils
 from .constants import *
 
-__version__ = '3.1.20'
+__version__ = '3.1.21'
 _logo = "icon.png"
 _references = ['CASTANODIEZ2012139']
 
@@ -106,28 +106,16 @@ def defineBinaries(cls, env):
             cudaMsgs.append(msg)
             useGpu = False
 
-        SW_EM = env.getEmFolder()
-        dyn_folder = 'dynamo-%s' % DEFAULT_VERSION
-
-        compile_cuda = "echo ' > %s' && " % preMsgs
-        if useGpu:
-            compile_cuda += "cd %s/%s/cuda && make clean && ./config.sh && " \
-                            "make all && " \
-                            "touch cuda_compiled && " % (SW_EM, dyn_folder)
-        compile_cuda += "echo ' > %s'" % cudaMsgs
-        commands = [(compile_cuda, '%s/%s/cuda/cuda_compiled' % (SW_EM, dyn_folder))]
-
-        env.addPackage('dynamo',
-                       version='1.146',
-                       tar='dynamo-1.146.tar.gz',
-                       commands=commands,
-                       default=False)
-
         # Dynamo 1.1.532
-        commands = [("cd cuda && make clean && ./config.sh %s && make all && touch cuda_compiled" % os.path.dirname(pwem.Config.CUDA_LIB), 'cuda/cuda_compiled')]
-        env.addPackage('dynamo', version='1.1.532',
+        commands = "./dynamo_setup_linux.sh "  # OpenMP commands
+        if useGpu:
+            # Cuda commands
+            commands += (f"&& cd cuda && ./config.sh {dirname(pwem.Config.CUDA_LIB)} && make clean && make motors && "
+                         f"make extended && touch cuda_compiled")
+        commands = [(commands, 'cuda/cuda_compiled')]
+        env.addPackage(DYNAMO_PROGRAM, version=DYNAMO_VERSION_1_1_532,
                        tar='dynamo-v-1.1.532_MCR-9.9.0_GLNXA64_withMCR.tar',
-                       createBuildDir = True,
+                       createBuildDir=True,
                        commands=commands,
                        default=True)
 
@@ -140,11 +128,11 @@ def checkDynamoVersion(cls):
         # Check the installed binary version
         dynamoVer = cls.getHome().split('-')[-1].replace('v', '')
         if int(dynamoVer.replace('.', '')) < MINIMUM_VERSION_NUM:
-           msg = ['The Dynamo version pointed by variable %s '
-                  '(%s) is not supported --> %s.\n\n'
-                  'Please, update the variable value or comment it in %s' %
-                  (DYNAMO_HOME, dynamoVer, DYNAMO_VERSION_1_1_532,
-                   pyworkflow.Config.SCIPION_CONFIG)]
+            msg = ['The Dynamo version pointed by variable %s '
+                   '(%s) is not supported --> %s.\n\n'
+                   'Please, update the variable value or comment it in %s' %
+                   (DYNAMO_HOME, dynamoVer, DYNAMO_VERSION_1_1_532,
+                    pyworkflow.Config.SCIPION_CONFIG)]
         return msg
 
     @classmethod

diff --git a/dynamo/constants.py b/dynamo/constants.py
@@ -28,7 +28,6 @@
 
 DYNAMO_PROGRAM = 'dynamo'
 DYNAMO_HOME = 'DYNAMO_HOME'
-DYNAMO_VERSION_1_146 = '1.146'
 DYNAMO_VERSION_1_1_532 = '1.1.532'
 DEFAULT_VERSION = DYNAMO_VERSION_1_1_532
 MINIMUM_VERSION_NUM = int(DYNAMO_VERSION_1_1_532.replace('.', ''))

diff --git a/dynamo/convert/convert.py b/dynamo/convert/convert.py
@@ -143,7 +143,7 @@ def dynTableLine2Subtomo(inLine, subtomo, subtomoSet=None, tomo=None, coordSet=N
         subtomoSet.append(subtomo)
 
 
-def readDynCoord(tableFile, coord3DSet, tomo):
+def readDynCoord(tableFile, coord3DSet, tomo, scaleFactor=1):
     with open(tableFile) as fhTable:
         for nline in fhTable:
             coordinate3d = Coordinate3D()
@@ -160,9 +160,9 @@ def readDynCoord(tableFile, coord3DSet, tomo):
             z = nline[25]
             groupId = nline[21]
             coordinate3d.setVolume(tomo)
-            coordinate3d.setX(float(x), const.BOTTOM_LEFT_CORNER)
-            coordinate3d.setY(float(y), const.BOTTOM_LEFT_CORNER)
-            coordinate3d.setZ(float(z), const.BOTTOM_LEFT_CORNER)
+            coordinate3d.setX(float(x) * scaleFactor, const.BOTTOM_LEFT_CORNER)
+            coordinate3d.setY(float(y) * scaleFactor, const.BOTTOM_LEFT_CORNER)
+            coordinate3d.setZ(float(z) * scaleFactor, const.BOTTOM_LEFT_CORNER)
             coordinate3d.setGroupId(int(groupId))
             coordinate3d.setMatrix(A)
             coord3DSet.append(coordinate3d)

diff --git a/dynamo/protocols/protocol_extraction.py b/dynamo/protocols/protocol_extraction.py
@@ -36,7 +36,7 @@
 from pyworkflow.protocol import PointerParam, EnumParam, IntParam, BooleanParam
 from pyworkflow.utils import removeExt
 from tomo.constants import BOTTOM_LEFT_CORNER, TR_DYNAMO
-from tomo.objects import SetOfSubTomograms, SubTomogram
+from tomo.objects import SetOfSubTomograms, SubTomogram, Coordinate3D, Tomogram
 from dynamo import Plugin, VLL_FILE
 from dynamo.convert import matrix2eulerAngles
 from tomo.protocols import ProtTomoBase
@@ -123,10 +123,10 @@ def _initialize(self):
         # Get the intersection between the tomograms and coordinates provided (this covers possible subsets made)
         inTomos = self.getInputTomograms()
         inCoords = self.inputCoordinates.get()
-        coordsPresentTomoIds = inCoords.getUniqueValues(['_tomoId'])
-        tomosPresentTsIds = inTomos.getUniqueValues(['_tsId'])
+        coordsPresentTomoIds = inCoords.getUniqueValues([Coordinate3D.TOMO_ID_ATTR])
+        tomosPresentTsIds = inTomos.getUniqueValues([Tomogram.TS_ID_FIELD])
         commonTomoIds = list(set(coordsPresentTomoIds).intersection(set(tomosPresentTsIds)))
-        self.tomoTsIdDict = {tomo.getTsId(): tomo for tomo in inTomos if tomo.getTsId() in commonTomoIds}
+        self.tomoTsIdDict = {tomo.getTsId(): tomo.clone() for tomo in inTomos if tomo.getTsId() in commonTomoIds}
         self.coordsFileName = self._getExtraPath('coords.txt')
         self.anglesFileName = self._getExtraPath('angles.txt')
         # Calculate the scale factor

diff --git a/setup.py b/setup.py
@@ -58,5 +58,8 @@
                       # Specify the Python versions you support here. In particular, ensure
                       # that you indicate whether you support Python 2, Python 3 or both.
                       'Programming Language :: Python :: 3'
+
+                      # Specify Framework
+                      'Framework :: Scipion :: 3'
                   ],
 )