8000 dose fixes by Vilax · Pull Request #152 · I2PC/scipion-em-xmipptomo · GitHub
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dose fixes #152

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Jul 27, 2023
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dose fixes #152

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20 changes: 18 additions & 2 deletions xmipptomo/protocols/protocol_extract_particlestacks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,12 @@ def _defineParams(self, form):
label='Box size',
help='The particle stack are extracted as squares. The box size defines the edge of the square',
important=True)

#TODO: This flag can be automitized
#form.addParam('defocusDir', BooleanParam,
# label='Defocus increase with z positive?', default=True,
# help='This flag must be put if the defocus increases or decreases along the z-axis. This is requires'
# 'to set the local CTF.')

form.addParam('invertContrast', BooleanParam,
label='Invert Contrast', default=True,
Expand Down Expand Up @@ -213,7 +219,8 @@ def writeMdTiltSeriesWithCTF(self, ts, tomoPath):
warningStr = ''
mdts = lib.MetaData()
for idxTS, idxCTF in zip(sorted_Idx_doseValueInTS, sorted_doseValueInCTF):
if doseValueInTS[idxTS] != doseValueInTSCTF[idxCTF]:
dose = doseValueInTS[idxTS]
if dose != doseValueInTSCTF[idxCTF]:
warningStr += '%s \n' % tsId
break
else:
Expand Down Expand Up @@ -245,6 +252,7 @@ def writeMdTiltSeriesWithCTF(self, ts, tomoPath):
nRow.setValue(lib.MDL_ANGLE_ROT, rot)
nRow.setValue(lib.MDL_SHIFT_X, Sx)
nRow.setValue(lib.MDL_SHIFT_Y, Sy)
nRow.setValue(lib.MDL_DOSE, dose)
nRow.addToMd(mdts)

fnts = os.path.join(tomoPath, "%s_ts.xmd" % tsId)
Expand Down Expand Up @@ -282,6 +290,8 @@ def extractStackStep(self, objId):
params += ' --coordinates %s' % fnCoords
params += ' --boxsize %i' % self.boxSize.get()
params += ' --sampling %f' % ts.getFirstItem().getSamplingRate()
#if self.defocusDir.get():
# params += ' --defocusPositive '
if self.setCTFinfo:
params += ' --setCTF '
if self.invertContrast.get():
Expand All @@ -304,6 +314,7 @@ def createOutputStep(self):
ts = self.tiltseries.get()
firstItem = ts.getFirstItem()
acquisitonInfo = firstItem.getAcquisition()
print(acquisitonInfo)
# TODO: Check the sampling if the tomograms are different than the picked ones
# TODO: Check the sampling rate if a downsampling option is implemented
outputSet = None
Expand All @@ -313,7 +324,7 @@ def createOutputStep(self):
bs = self.boxSize.get()
self.outputParticleStackSet.setDim(ImageDim(bs, bs, bs))
self.outputParticleStackSet.setAnglesCount(ts.getAnglesCount())
if firstItem.getAcquisition():
if acquisitonInfo:
acquisition = TomoAcquisition()
acquisition.setAngleMin(acquisitonInfo.getAngleMin())
acquisition.setAngleMax(acquisitonInfo.getAngleMax())
Expand All @@ -336,9 +347,12 @@ def createOutputStep(self):
if self.asSPAparticles:
fn = self._getExtraPath('allparticles.xmd')
outputSet = self._createSetOfParticles()
outputSet.setAcquisition(acquisitonInfo)
self.createMdWithall2DTiltParticles(fn)
#TODO set dose per particle
readSetOfParticles(fn, outputSet)
outputSet.setSamplingRate(self.tiltseries.get().getSamplingRate())
outputSet.write()

self._defineOutputs(outputParticles=outputSet)
self._defineSourceRelation(self.coords, outputSet)
Expand Down Expand Up @@ -366,6 +380,7 @@ def createMdWithall2DTiltParticles(self, fn):
rot = row.getValue(lib.MDL_ANGLE_ROT)
Sx = row.getValue(lib.MDL_SHIFT_X)
Sy = row.getValue(lib.MDL_SHIFT_Y)
dose = row.getValue(lib.MDL_DOSE)

rowglobal.setValue(md.MDL_IMAGE, fnImg[0] + '@' + os.path.join(basemdpath, fnImg[1]))
rowglobal.setValue(md.MDL_TSID, ts_orig)
Expand All @@ -377,6 +392,7 @@ def createMdWithall2DTiltParticles(self, fn):
rowglobal.setValue(lib.MDL_ANGLE_PSI, psi)
rowglobal.setValue(lib.MDL_SHIFT_X, Sx)
rowglobal.setValue(lib.MDL_SHIFT_Y, Sy)
rowglobal.setValue(lib.MDL_DOSE, dose)
rowglobal.addToMd(mdAllParticles)
mdAllParticles.write(fn)

Expand Down
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