Source code for topaz.convert

# **************************************************************************
# *
# * Authors:     J.M. De la Rosa Trevin ( [1]
# *              Peter Horvath ( [2]
# *
# * [1] SciLifeLab, Stockholm University
# * [2] I2PC
# *
# * 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
# * the Free Software Foundation; either version 3 of the License, or
# * (at your option) any later version.
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# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
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# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
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# *  All comments concerning this program package may be sent to the
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# **************************************************************************

import csv
import os

import pyworkflow.utils as pwutils
from pyworkflow.object import Float
from pwem.emlib.image import ImageHandler
from pwem.objects import Coordinate

from topaz import constants

[docs]class CsvImageList: """ Handler class to write a list of images as expected by topaz. """ def __init__(self, filename, mode='r', **kwargs): self.__file = None if mode == 'r': self.__file = open(filename, 'r') self.__reader = csv.reader(self.__file, delimiter='\t') elif mode == 'w': self.__file = open(filename, 'w') self.__writer = csv.writer(self.__file, delimiter='\t') self.__writer.writerow(kwargs['columns']) def _addRow(self, *values): self.__writer.writerow(values)
[docs] def close(self): self.__file.close()
def __iter__(self): it = iter(self.__reader) # Just discard the first row self.__columns = next(it) return it
[docs]class CsvMicrographList(CsvImageList): """ Handler class to write a list of micrographs as expected by topaz. """ def __init__(self, filename, mode='r'): CsvImageList.__init__(self, filename, mode, columns=['image_name', 'path'])
[docs] def addMic(self, micId, micPath): self._addRow('%06d' % micId, micPath)
[docs]class CsvCoordinateList(CsvImageList): """ Handler class to write a list of particles as expected by topaz. """ def __init__(self, filename, mode='r', score=False): columns = ['image_name', 'x_coord', 'y_coord'] if score: columns.append('score') CsvImageList.__init__(self, filename, mode, columns=columns)
[docs] def addCoord(self, micId, x, y): self._addRow('%06d' % micId, x, y)
[docs]def convertMicrographs(micList, micDir): """ Convert (or simply link) input micrographs into the given directory in a format that is compatible with Topaz. """ ih = ImageHandler() ext = pwutils.getExt(micList[0].getFileName()) def _convert(mic, newName): ih.convert(mic, os.path.join(micDir, newName)) def _link(mic, newName): pwutils.createAbsLink(os.path.abspath(mic.getFileName()), os.path.join(micDir, newName)) if ext in constants.TOPAZ_SUPPORTED_FORMATS: func = _link else: func = _convert ext = '.mrc' for mic in micList: func(mic, getMicIdName(mic, suffix=ext))
[docs]def readSetOfCoordinates(coordinatesCsvFn, micSet, coordSet, scale): """ Read coordinates produced by Topaz. Coordinates are expected in a single csv file, with the following columns: first: image_name (mic id) second: x_coord third: y_coord forth: score """ csv = CsvCoordinateList(coordinatesCsvFn, score=True) lastMicId = None coord = Coordinate() coord._topazScore = Float() micDict = {} # loop to generate a dictionary --> micBaseName : Micrograph for mic in micSet: micNew = mic.clone() micDict[mic.getObjId()] = micNew #loop the Topaz outputfile for row in csv: micId = int(row[0]) if micId != lastMicId: mic = micDict[micId] if mic is None: print("Missing id: ", micId) else: coord.setMicrograph(mic) lastMicId = micId coord.setPosition(int(round(float(row[1])*scale)), int(round(float(row[2])*scale))) coord._topazScore.set(float(row[3])) coord.setObjId(None) coordSet.append(coord) csv.close()
[docs]def getMicIdName(mic, suffix=''): """ Return a name for the micrograph based on its IDs. """ return '%d%s' % (mic.getObjId(), suffix)