Example #1
0
    def show(self, form):
        autopickProt = form.protocol
        micSet = autopickProt.getInputMicrographs()
        if not micSet:
            print 'must specify input micrographs'
            return
        project = autopickProt.getProject()
        micfn = micSet.getFileName()
        coordsDir = project.getTmpPath(micSet.getName())
        cleanPath(coordsDir)
        makePath(coordsDir)

        pickerProps = os.path.join(coordsDir, 'picker.conf')
        f = open(pickerProps, "w")
        params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
        args = {
            "params": ','.join(params),
            "preprocess": "%s sxprocess.py" % pw.getScipionScript(),
            "picker": "%s e2boxer.py" % pw.getScipionScript(),
            "convert": pw.join('apps', 'pw_convert.py'),
            'coordsDir': coordsDir,
            'micsSqlite': micSet.getFileName(),
            "boxSize": autopickProt.boxSize,
            "lowerThreshold": autopickProt.lowerThreshold,
            "higherThreshold": autopickProt.higherThreshold,
            "gaussWidth": autopickProt.gaussWidth,
            "extraParams": autopickProt.extraParams
        }

        f.write("""
        parameters = %(params)s
        boxSize.value = %(boxSize)s
        boxSize.label = Box Size
        boxSize.help = some help
        lowerThreshold.value =  %(lowerThreshold)s
        lowerThreshold.label = Lower Threshold
        lowerThreshold.help = some help
        higherThreshold.help = some help
        higherThreshold.value =  %(higherThreshold)s
        higherThreshold.label = Higher Threshold
        gaussWidth.help = some help
        gaussWidth.value =  %(gaussWidth)s
        gaussWidth.label = Gauss Width
        runDir = %(coordsDir)s
        preprocessCommand = %(preprocess)s demoparms --makedb=thr_low=%%(lowerThreshold):thr_hi=%%(higherThreshold):boxsize=%%(boxSize):gauss_width=%%(gaussWidth):%(extraParams)s
        autopickCommand = %(picker)s --gauss_autoboxer=demoparms --write_dbbox --boxsize=%%(boxSize) --norm=normalize.ramp.normvar %%(micrograph) 
        convertCommand = %(convert)s --coordinates --from eman2 --to xmipp --input  %(micsSqlite)s --output %(coordsDir)s
        """ % args)
        f.close()
        process = CoordinatesObjectView(project,
                                        micfn,
                                        coordsDir,
                                        autopickProt,
                                        pickerProps=pickerProps).show()
        process.wait()
        myprops = readProperties(pickerProps)

        if myprops['applyChanges'] == 'true':
            for param in params:
                form.setVar(param, myprops[param + '.value'])
Example #2
0
    def show(self, form):
        autopickProt = form.protocol
        micSet = autopickProt.getInputMicrographs()
        if not micSet:
            print 'must specify input micrographs'
            return
        project = autopickProt.getProject()
        micfn = micSet.getFileName()
        coordsDir = project.getTmpPath(micSet.getName())
        cleanPath(coordsDir)
        makePath(coordsDir)
        # Get current values of the properties
        #         micfn = os.path.join(coordsDir, 'micrographs.xmd')
        #         writeSetOfMicrographs(micSet, micfn)
        dogpickerProps = os.path.join(coordsDir, 'picker.conf')
        f = open(dogpickerProps, "w")

        args = {
            "dogpicker":
            os.path.join(os.environ['DOGPICKER_HOME'], "ApDogPicker.py"),
            "convert":
            pw.join('apps', 'pw_convert.py'),
            'coordsDir':
            coordsDir,
            'micsSqlite':
            micSet.getFileName(),
            "diameter":
            autopickProt.diameter,
            "threshold":
            autopickProt.threshold,
            "apix":
            micSet.getSamplingRate()
        }

        f.write("""
        parameters = diameter,threshold
        diameter.value = %(diameter)s
        diameter.label = Diameter
        diameter.help = some help
        threshold.value =  %(threshold)s
        threshold.label = Threshold
        threshold.help = some help
        autopickCommand = %(dogpicker)s  --thresh=%%(threshold) --diam=%%(diameter) --apix=%(apix)s  --image=%%(micrograph) --outfile=%(coordsDir)s/%%(micrographName).txt 
        convertCommand = %(convert)s --coordinates --from dogpicker --to xmipp --input  %(micsSqlite)s --output %(coordsDir)s
        """ % args)
        f.close()
        process = CoordinatesObjectView(project,
                                        micfn,
                                        coordsDir,
                                        autopickProt,
                                        pickerProps=dogpickerProps).show()
        process.wait()
        # Check if the wizard changes were accepted or just canceled

        myprops = readProperties(dogpickerProps)

        if myprops['applyChanges'] == 'true':
            form.setVar('diameter', myprops['diameter.value'])
            form.setVar('threshold', myprops['threshold.value'])
Example #3
0
    def show(self, form):
        autopickProt = form.protocol
        micSet = autopickProt.getInputMicrographs()
        if not micSet:
            print 'must specify input micrographs'
            return
        project = autopickProt.getProject()
        micfn = micSet.getFileName()
        coordsDir = project.getTmpPath(micSet.getName())
        cleanPath(coordsDir)
        makePath(coordsDir)
        
        pickerProps = os.path.join(coordsDir, 'picker.conf')
        f = open(pickerProps, "w")
        params = ['boxSize', 'lowerThreshold', 'higherThreshold', 'gaussWidth']
        args = {
          "params": ','.join(params),
          "preprocess" : os.path.join(os.environ['SCIPION_HOME'], "scipion sxprocess.py"),
          "picker" : os.path.join(os.environ['SCIPION_HOME'], "scipion e2boxer.py"),
          "convert" : os.path.join(os.environ['SCIPION_HOME'], os.path.join('pyworkflow','apps', 'pw_convert.py')),
          'coordsDir':coordsDir,
          'micsSqlite': micSet.getFileName(),
          "boxSize": autopickProt.boxSize,
          "lowerThreshold": autopickProt.lowerThreshold,
          "higherThreshold": autopickProt.higherThreshold,
          "gaussWidth": autopickProt.gaussWidth,
          "extraParams":autopickProt.extraParams
          }


        f.write("""
        parameters = %(params)s
        boxSize.value = %(boxSize)s
        boxSize.label = Box Size
        boxSize.help = some help
        lowerThreshold.value =  %(lowerThreshold)s
        lowerThreshold.label = Lower Threshold
        lowerThreshold.help = some help
        higherThreshold.help = some help
        higherThreshold.value =  %(higherThreshold)s
        higherThreshold.label = Higher Threshold
        gaussWidth.help = some help
        gaussWidth.value =  %(gaussWidth)s
        gaussWidth.label = Gauss Width
        runDir = %(coordsDir)s
        preprocessCommand = %(preprocess)s demoparms --makedb=thr_low=%%(lowerThreshold):thr_hi=%%(higherThreshold):boxsize=%%(boxSize):gauss_width=%%(gaussWidth):%(extraParams)s
        autopickCommand = %(picker)s --gauss_autoboxer=demoparms --write_dbbox --boxsize=%%(boxSize) --norm=normalize.ramp.normvar %%(micrograph) 
        convertCommand = %(convert)s --coordinates --from eman2 --to xmipp --input  %(micsSqlite)s --output %(coordsDir)s
        """ % args)
        f.close()
        process = CoordinatesObjectView(project, micfn, coordsDir, autopickProt, pickerProps=pickerProps).show()
        process.wait()
        myprops = readProperties(pickerProps)
        for param in params:
            form.setVar(param, myprops[param + '.value'])
Example #4
0
    def show(self, form):
        autopickProt = form.protocol
        micSet = autopickProt.getInputMicrographs()
        if not micSet:
            print 'must specify input micrographs'
            return
        project = autopickProt.getProject()
        micfn = micSet.getFileName()
        coordsDir = project.getTmpPath(micSet.getName())
        cleanPath(coordsDir)
        makePath(coordsDir)
        # Get current values of the properties
#         micfn = os.path.join(coordsDir, 'micrographs.xmd')
#         writeSetOfMicrographs(micSet, micfn)
        dogpickerProps = os.path.join(coordsDir, 'picker.conf')
        f = open(dogpickerProps, "w")

        args = {
          "dogpicker" : os.path.join(os.environ['DOGPICKER_HOME'], "ApDogPicker.py"),
          "convert" : pw.join('apps', 'pw_convert.py'),
          'coordsDir': coordsDir,
          'micsSqlite': micSet.getFileName(),
          "diameter": autopickProt.diameter,
          "threshold": autopickProt.threshold,
          "apix": micSet.getSamplingRate()
          }


        f.write("""
        parameters = diameter,threshold
        diameter.value = %(diameter)s
        diameter.label = Diameter
        diameter.help = some help
        threshold.value =  %(threshold)s
        threshold.label = Threshold
        threshold.help = some help
        autopickCommand = %(dogpicker)s  --thresh=%%(threshold) --diam=%%(diameter) --apix=%(apix)s  --image=%%(micrograph) --outfile=%(coordsDir)s/%%(micrographName).txt 
        convertCommand = %(convert)s --coordinates --from dogpicker --to xmipp --input  %(micsSqlite)s --output %(coordsDir)s
        """ % args)
        f.close()
        process = CoordinatesObjectView(project, micfn, coordsDir, autopickProt,
                                        mode=CoordinatesObjectView.MODE_AUTOMATIC,
                                        pickerProps=dogpickerProps).show()
        process.wait()
        # Check if the wizard changes were accepted or just canceled

        myprops = readProperties(dogpickerProps)

        if myprops['applyChanges'] == 'true':
            form.setVar('diameter', myprops['diameter.value'])
            form.setVar('threshold', myprops['threshold.value'])