# **************************************************************************
# *
# * Authors: Pablo Conesa (pconesa@cnb.csic.es)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# * GNU General Public License for more details.
# *
# * 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
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'scipion@cnb.csic.es'
# *
# **************************************************************************
"""
This modules contains file handlers to be registered in the scipion file browser
"""
import os
import pwem
import pyworkflow.utils as pwutils
from pwem.convert import Ccp4Header
from pyworkflow import gui
from pyworkflow.gui.browser import FileHandler, isStandardImage
from pwem import emlib
from pwem.emlib.image.image_handler import ImageHandler
import logging
logger = logging.getLogger(__name__)
[docs]class ImageFileHandler(FileHandler):
_image = emlib.Image()
_index = ''
def _getImageString(self, filename):
if isStandardImage(filename):
return "Image file."
x, y, z, n = ImageHandler.getDimensions(filename)
objType = 'Image'
objFileType = "link" if os.path.islink(filename) else "file"
dimMsg = "*%(objType)s %(objFileType)s*\n dimensions: %(x)d x %(y)d"
expMsg = "Columns x Rows "
if z > 1:
dimMsg += " x %(z)d"
expMsg += " x Slices"
objType = 'Volume'
if n > 1:
dimMsg += " x %(n)d"
expMsg += " x Objects"
objType = 'Stack'
if Ccp4Header.isCompatible(filename):
ccp4Reader= Ccp4Header(filename, readHeader=True)
expMsg += "\nHeader info: \nSampling rate: %1.2f, %1.2f, %1.2f" % ccp4Reader.getSampling()
expMsg += "\nOrigin: %1.2f, %1.2f, %1.2f" % ccp4Reader.getOrigin()
return (dimMsg + "\n" + expMsg) % locals()
def _getImagePreview(self, filename):
# If file size if big
if pwutils.getFileSize(filename) > (pwem.Config.MAX_PREVIEW_FILE_SIZE * 1024*1024):
return
dim = 128
if isStandardImage(filename):
self.tkImg = gui.getImage(os.path.abspath(filename),
tkImage=True, maxheight=dim)
else:
fn = self._index + filename
self.tkImg = getTkImage(self._image, fn, dim)
return self.tkImg
[docs] def getFilePreview(self, objFile):
fn = objFile.getPath()
return self._getImagePreview(fn), self._getImageString(fn)
[docs] def getFileActions(self, objFile):
from .views import DataView
fn = objFile.getPath()
return [('Open with Xmipp viewer', lambda: DataView(fn).show(),
pwutils.Icon.ACTION_VISUALIZE)]
[docs]class ParticleFileHandler(ImageFileHandler):
[docs] def getFileIcon(self, objFile):
return pwutils.Icon.FILE_IMAGE if not objFile.isLink() else pwutils.Icon.FILE_IMAGE_LINK
[docs]class VolFileHandler(ImageFileHandler):
[docs] def getFileIcon(self, objFile):
return pwutils.Icon.FILE_VOL
[docs]class StackHandler(ImageFileHandler):
_index = '1@'
[docs] def getFileIcon(self, objFile):
return pwutils.Icon.FILE_STACK if not objFile.isLink() else pwutils.Icon.FILE_STACK_LINK
[docs]class ImajeJFileHandler(FileHandler):
[docs] def getFileActions(self, objFile):
from pyworkflow.viewer import CommandView
fn = objFile.getPath()
fijiPath = pwem.Config.IMAGEJ_BINARY_PATH
if fijiPath:
cmd = '%s "%s"' % (fijiPath, fn)
return [('Open with ImageJ/Fiji', lambda: CommandView(cmd).show(),
pwutils.Icon.ACTION_VISUALIZE)]
[docs] def getFileIcon(self, objFile):
return 'file_image.gif' if not objFile.isLink() else 'file_image_link.gif'
[docs]class ChimeraHandler(FileHandler):
[docs] def getFileActions(self, objFile):
from .viewer_chimera import ChimeraView
fn = objFile.getPath()
return [('Open with Chimera', lambda: ChimeraView(fn).show(),
pwutils.Icon.ACTION_VISUALIZE)]
[docs] def getFileIcon(self, objFile):
return pwutils.Icon.TXT_FILE
[docs]class MdFileHandler(ImageFileHandler):
[docs] def getFileIcon(self, objFile):
if objFile.isLink():
return pwutils.Icon.FILE_METADATA_LINK
else:
return pwutils.Icon.FILE_METADATA
def _getImgPath(self, mdFn, imgFn):
""" Get ups and ups until finding the relative location to images. """
path = os.path.dirname(mdFn)
index, fn = emlib.FileName(imgFn).decompose()
while path and path != '/':
newFn = os.path.join(path, fn)
if os.path.exists(newFn):
if index:
newFn = '%d@%s' % (index, newFn)
return newFn
path = os.path.dirname(path)
return None
def _getMdString(self, filename, block=None):
md = emlib.MetaData()
if block:
md.read(block + '@' + filename)
else:
md.read(filename, 1)
labels = md.getActiveLabels()
msg = "Metadata items: *%d*\n" % md.getParsedLines()
msg += "Metadata labels: " + ''.join(
["\n - %s" % emlib.label2Str(l)
for l in labels])
imgPath = None
for label in labels:
if emlib.labelIsImage(label):
imgPath = self._getImgPath(filename,
md.getValue(label, md.firstObject()))
if imgPath is None or not os.path.exists(imgPath):
imgPath = None
break
# If there is an image and is not too big
if imgPath and pwutils.getFileSize(imgPath) < (pwem.Config.MAX_PREVIEW_FILE_SIZE * 1024*1024):
self._imgPreview = self._getImagePreview(imgPath)
self._imgInfo = self._getImageString(imgPath)
return msg
[docs] def getFilePreview(self, objFile):
self._imgPreview = None
self._imgInfo = None
filename = objFile.getPath()
ext = pwutils.getExt(filename)
if ext == '.xmd' or ext == '.ctfparam' or ext == '.pos' or ext == '.doc':
msg = "*Metadata File* "
blocks = emlib.getBlocksInMetaDataFile(filename)
nblocks = len(blocks)
if nblocks <= 1:
mdStr = self._getMdString(filename)
msg += " (single block)\n"
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += '\n' + mdStr
else:
mdStr = self._getMdString(filename, blocks[0])
msg += " (%d blocks) " % nblocks
if self._imgInfo:
msg += "\nFirst item: \n" + self._imgInfo
msg += "\nFirst block: \n" + mdStr
msg += "\nAll blocks:" + ''.join(
["\n - %s" % b for b in blocks])
elif ext == '.star':
msg = "*Relion STAR file* \n"
msg += self._getMdString(filename)
return self._imgPreview, msg
# Image methods for filehandlers
[docs]def getPILImage(imageXmipp, dim=None, normalize=True):
""" Given an image read by Xmipp, convert it to PIL. """
from PIL import Image
if normalize:
imageXmipp.convert2DataType(emlib.DT_UCHAR, emlib.CW_ADJUST)
imageData = imageXmipp.getData()
image = Image.fromarray(imageData)
if dim:
size = int(dim), int(dim)
image.thumbnail(size, Image.ANTIALIAS)
return image
[docs]def getTkImage(imageXmipp, filename, dim):
from PIL import ImageTk
imageXmipp.readPreview(filename, dim)
return ImageTk.PhotoImage(getPILImage(imageXmipp))
[docs]def getImageFromPath(imagePath):
""" Read an image using Xmipp, convert to PIL
and then return as expected by Tk.
"""
img = emlib.Image(imagePath)
imgPIL = getPILImage(img)
from PIL import ImageTk
imgTk = ImageTk.PhotoImage(imgPIL)
return imgTk