Source code for xmipp3.convert.io_coordinates

import os

from pyworkflow.utils.path import cleanPath
from pwem.objects import SetOfCoordinates

from xmipp3.convert import readSetOfCoordinates


[docs]def readSetOfCoordsFromPosFnames(posDir, setOfInputCoords, sqliteOutName, write=True): """ posDir: path where there are .pos files with coordinates setOfInputCoords. Set to find micrographs sqliteOutName. Path where sqlite map will be created. Warning, it overwrites content """ inputMics = setOfInputCoords.getMicrographs() cleanPath(sqliteOutName) setOfOutputCoordinates= SetOfCoordinates(filename= sqliteOutName) setOfOutputCoordinates.setMicrographs(inputMics) setOfOutputCoordinates.setBoxSize(setOfInputCoords.getBoxSize()) readSetOfCoordinates(posDir, micSet=inputMics, coordSet=setOfOutputCoordinates, readDiscarded=False) if write: setOfOutputCoordinates.write() return setOfOutputCoordinates
[docs]def writeCoordsListToPosFname(mic_fname, list_x_y, outputRoot): s = """# XMIPP_STAR_1 * # data_header loop_ _pickingMicrographState Auto data_particles loop_ _xcoor _ycoor """ baseName = os.path.basename(mic_fname).split(".")[0] print("%d %s %s"%(len(list_x_y), mic_fname, os.path.join(outputRoot, baseName+".pos"))) if len(list_x_y)>0: with open(os.path.join(outputRoot, baseName+".pos"), "w") as f: f.write(s) for x, y in list_x_y: f.write(" %d %d\n" % (x, y))
[docs]def writeCoordsListToRawText(mic_fname, list_x_y, outputRoot): baseName= os.path.basename(mic_fname).split(".")[0] with open(os.path.join(outputRoot, baseName+"_raw_coords.txt"), "w") as f: f.write("#%s %s\n"%(baseName, mic_fname)) for x, y in list_x_y: f.write("%d %d\n"%(x, y))