Merge pull request #185 from I2PC/fixes

dose filter, removing extract stacks: fixed for merging base
I2PC · May 29, 2024 · 76891ac · 76891ac
2 parents aa81664 + 8901c01
commit 76891ac
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 459 deletions.
diff --git a/xmipptomo/protocols/__init__.py b/xmipptomo/protocols/__init__.py
@@ -35,7 +35,6 @@
 from .protocol_dose_filter import XmippProtDoseFilter
 from .protocol_filter_coordinates_by_map import XmippProtFilterCoordinatesByMap
 from .protocol_crop_tomograms import XmippProtCropTomograms
-from .protocol_extract_particlestacks import XmippProtExtractParticleStacks
 from .protocol_extract_subtomos import XmippProtExtractSubtomos
 from .protocol_flexalign import XmippProtTsFlexAlign
 from .protocol_peak_high_contrast import XmippProtPeakHighContrast

diff --git a/xmipptomo/protocols/protocol_dose_filter.py b/xmipptomo/protocols/protocol_dose_filter.py
@@ -34,6 +34,7 @@
 import pwem.emlib.metadata as md
 import pwem.emlib as emlib
 from pwem.protocols import EMProtocol
+from pyworkflow.utils import getExt
 
 from tomo.protocols.protocol_base import ProtTomoImportFiles
 from tomo.protocols import ProtTomoBase
@@ -42,6 +43,8 @@
 SCIPION_IMPORT = 0
 FIXED_DOSE = 1
 
+EXT_MRCS = '.mrcs'
+
 
 class XmippProtDoseFilter(ProtTomoImportFiles, EMProtocol, ProtTomoBase):
     """
@@ -61,13 +64,13 @@ def _defineParams(self, form):
                       params.PointerParam,
                       pointerClass='SetOfTiltSeries',
                       important=True,
-                      label='Input set of tilt-series to be filtered.')
+                      label='Tilt-series to be filtered.')
 
         form.addParam('initialDose',
                       params.FloatParam,
                       default=0.0,
                       expertLevel=params.LEVEL_ADVANCED,
-                      label='Initial dose (e/sq A)',
+                      label='Initial dose (e/A^2)',
                       help='Dose applied before any of the images in the input file were taken; this value will be '
                            'added to all the prior dose values, however they were obtained.')
 
@@ -93,12 +96,16 @@ def doseFilterStep(self, tsObjId):
 
         firstItem = ts.getFirstItem()
 
-        fnMd = 'image_and_dose.xmd'
+        fnMd = self._getExtraPath(tsId, 'image_and_dose.xmd')
         mdDose = md.MetaData()
         idx = 1
         for ti in ts:
             doseValue = ti.getAcquisition().getAccumDose()
             fn = ti.getFileName()
+            ext = getExt(fn)
+            if ext == '.mrc' or ext == '.map':
+                fn = fn+':mrcs'
+
             strimg = str(idx) + '@' + fn
             idx = idx + 1
 
@@ -110,8 +117,8 @@ def doseFilterStep(self, tsObjId):
         mdDose.write(fnMd)
 
         params = ' -i %s '          % fnMd
-        params += ' -o %s '         % (os.path.join(extraPrefix, os.path.splitext(os.path.basename(ts.getFileName()))[0]  + '.mrcs'))
-        params += ' --sampling %s' % self.inputSetOfTiltSeries.get().getSamplingRate()
+        params += ' -o %s '         % (os.path.join(extraPrefix, os.path.splitext(os.path.basename(ts.getFileName()))[0]  + EXT_MRCS))
+        params += ' --sampling %s ' % self.inputSetOfTiltSeries.get().getSamplingRate()
         params += ' --voltage %f '  % ts.getAcquisition().getVoltage()
 
         self.runJob('xmipp_tomo_tiltseries_dose_filter', params)