/usr/lib/python2.7/dist-packages/fabio/fabioimage.py is in python-fabio 0.3.0+dfsg-1build1.
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#
# Project: X-ray image reader
# https://github.com/kif/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# 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, see <http://www.gnu.org/licenses/>.
#
"""
Authors: Henning O. Sorensen & Erik Knudsen
Center for Fundamental Research: Metal Structures in Four Dimensions
Risoe National Laboratory
Frederiksborgvej 399
DK-4000 Roskilde
email:erik.knudsen@risoe.dk
and Jon Wright, Jerome Kieffer: ESRF
"""
# get ready for python3
from __future__ import with_statement, print_function, absolute_import, division
import os
import logging
import sys
import tempfile
import threading
logger = logging.getLogger("fabioimage")
import numpy
try:
from PIL import Image
except ImportError:
logger.warning("PIL is not installed ... trying to do without")
Image = None
from . import fabioutils, converters
from .fabioutils import six
try:
from collections import OrderedDict
except ImportError:
from .third_party.ordereddict import OrderedDict
class FabioMeta(type):
"""
Metaclass used to register all image classes inheriting from fabioImage
"""
# we use __init__ rather than __new__ here because we want
# to modify attributes of the class *after* they have been
# created
def __init__(cls, name, bases, dct):
cls.registry[name.lower()] = cls
super(FabioMeta, cls).__init__(name, bases, dct)
class FabioImage(six.with_metaclass(FabioMeta, object)):
"""
A common object for images in fable
Contains a numpy array (.data) and dict of meta data (.header)
"""
_need_a_seek_to_read = False
_need_a_real_file = False
registry = OrderedDict() # list of child classes ...
@classmethod
def factory(cls, name):
"""
A kind of factory...
@param name: name of the class to instanciate
@type name: str
@return: an instance of the class
@rtype: fabioimage
"""
name = name.lower()
obj = None
if name in cls.registry:
obj = cls.registry[name]()
else:
msg = ("FileType %s is unknown !, "
"please check if the filename exists or select one from %s" % (name, cls.registry.keys()))
logger.error(msg)
raise RuntimeError(msg)
return obj
def __init__(self, data=None , header=None):
"""
Set up initial values
"""
self._classname = None
self._dim1 = self._dim2 = self._bpp = 0
self._bytecode = None
if type(data) in fabioutils.StringTypes:
raise Exception("fabioimage.__init__ bad argument - " + \
"data should be numpy array")
self.data = self.check_data(data)
self.pilimage = None
self.header = self.check_header(header)
# cache for image statistics
self.mean = self.maxval = self.stddev = self.minval = None
# Cache roi
self.roi = None
self.area_sum = None
self.slice = None
# New for multiframe files
self.nframes = 1
self.currentframe = 0
self.filename = None
self.filenumber = None
def get_header_keys(self):
return list(self.header.keys())
def set_header_keys(self, value):
pass
header_keys = property(get_header_keys, set_header_keys)
def get_dim1(self):
"Getter for dim1: data superseeds _dim1"
if self.data is not None:
try:
return self.data.shape[1]
except IndexError as err:
print(err)
print(self.data)
return self._dim1
else:
return self._dim1
def set_dim1(self, value):
"Setter for dim1"
self._dim1 = value
dim1 = property(get_dim1, set_dim1)
def get_dim2(self):
"Getter for dim2: data superseeds _dim2"
if self.data is not None:
return self.data.shape[0]
else:
return self._dim2
def set_dim2(self, value):
"Setter for dim2"
self._dim2 = value
dim2 = property(get_dim2, set_dim2)
def get_bpp(self):
"Getter for bpp: data superseeds _bpp"
if self.data is not None:
return numpy.dtype(self.data.dtype).itemsize
elif self._bytecode is not None:
return numpy.dtype(self._bytecode).itemsize
else:
return self._bpp
def set_bpp(self, value):
"Setter for bpp"
self._bpp = value
bpp = property(get_bpp, set_bpp)
def get_bytecode(self):
"Getter for bpp: data superseeds _bytecode"
if self.data is not None:
return self.data.dtype.type
else:
return self._bytecode
def set_bytecode(self, value):
"Setter for bpp"
self._bytecode = value
bytecode = property(get_bytecode, set_bytecode)
@staticmethod
def check_header(header=None):
"""
Empty for fabioimage but may be populated by others classes
@param header: dict like object
@return: Ordered dict
"""
if header is None:
return OrderedDict()
else:
return OrderedDict(header)
@staticmethod
def check_data(data=None):
"""
Empty for fabioimage but may be populated by others classes,
especially for format accepting only integers
@param data: array like
@return: numpy array or None
"""
if data is None:
return None
else:
return data
def getclassname(self):
"""
Retrieves the name of the class
@return: the name of the class
"""
if self._classname is None:
self._classname = str(self.__class__).replace("<class '", "").replace("'>", "").split(".")[-1]
return self._classname
classname = property(getclassname)
def getframe(self, num):
""" returns the file numbered 'num' in the series as a fabioimage """
if self.nframes == 1:
# single image per file
from .openimage import openimage
return openimage(fabioutils.jump_filename(self.filename, num))
raise Exception("getframe out of range")
def previous(self):
""" returns the previous file in the series as a fabioimage """
from .openimage import openimage
return openimage(fabioutils.previous_filename(self.filename))
def next(self):
""" returns the next file in the series as a fabioimage """
from .openimage import openimage
return openimage(
fabioutils.next_filename(self.filename))
def toPIL16(self, filename=None):
"""
Convert to Python Imaging Library 16 bit greyscale image
"""
if not Image:
raise RuntimeError("PIL is not installed !!! ")
if filename:
self.read(filename)
if self.pilimage is not None:
return self.pilimage
# mode map
size = self.data.shape[:2][::-1]
typmap = {
'float32' : "F" ,
'int32' : "F;32NS" ,
'uint32' : "F;32N" ,
'int16' : "F;16NS" ,
'uint16' : "F;16N" ,
'int8' : "F;8S" ,
'uint8' : "F;8" }
if self.data.dtype.name in typmap:
mode2 = typmap[ self.data.dtype.name ]
mode1 = mode2[0]
else:
raise RuntimeError("Unknown numpy type: %s" % (self.data.dtype.type))
dats = self.data.tostring()
self.pilimage = Image.frombuffer(mode1, size, dats, "raw", mode2, 0, 1)
return self.pilimage
def getheader(self):
""" returns self.header """
return self.header
def getmax(self):
""" Find max value in self.data, caching for the future """
if self.maxval is None:
if self.data is not None:
self.maxval = self.data.max()
return self.maxval
def getmin(self):
""" Find min value in self.data, caching for the future """
if self.minval is None:
if self.data is not None:
self.minval = self.data.min()
return self.minval
def make_slice(self, coords):
"""
Convert a len(4) set of coords into a len(2)
tuple (pair) of slice objects
the latter are immutable, meaning the roi can be cached
"""
assert len(coords) == 4
if len(coords) == 4:
# fabian edfimage preference
if coords[0] > coords[2]:
coords[0:3:2] = [coords[2], coords[0]]
if coords[1] > coords[3]:
coords[1:4:2] = [coords[3], coords[1]]
# in fabian: normally coordinates are given as (x,y) whereas
# a matrix is given as row,col
# also the (for whichever reason) the image is flipped upside
# down wrt to the matrix hence these tranformations
fixme = (self.dim2 - coords[3] - 1,
coords[0] ,
self.dim2 - coords[1] - 1,
coords[2])
return (slice(int(fixme[0]), int(fixme[2]) + 1) ,
slice(int(fixme[1]), int(fixme[3]) + 1))
def integrate_area(self, coords):
"""
Sums up a region of interest
if len(coords) == 4 -> convert coords to slices
if len(coords) == 2 -> use as slices
floor -> ? removed as unused in the function.
"""
if self.data is None:
# This should return NAN, not zero ?
return 0
if len(coords) == 4:
sli = self.make_slice(coords)
elif len(coords) == 2 and isinstance(coords[0], slice) and \
isinstance(coords[1], slice):
sli = coords
if sli == self.slice and self.area_sum is not None:
pass
elif sli == self.slice and self.roi is not None:
self.area_sum = self.roi.sum(dtype=numpy.float)
else:
self.slice = sli
self.roi = self.data[ self.slice ]
self.area_sum = self.roi.sum(dtype=numpy.float)
return self.area_sum
def getmean(self):
""" return the mean """
if self.mean is None:
self.mean = self.data.mean(dtype=numpy.double)
return self.mean
def getstddev(self):
""" return the standard deviation """
if self.stddev is None:
self.stddev = self.data.std(dtype=numpy.double)
return self.stddev
def add(self, other):
"""
Add another Image - warning, does not clip to 16 bit images by default
"""
if not hasattr(other, 'data'):
logger.warning('edfimage.add() called with something that ' + \
'does not have a data field')
assert self.data.shape == other.data.shape , \
'incompatible images - Do they have the same size?'
self.data = self.data + other.data
self.resetvals()
def resetvals(self):
""" Reset cache - call on changing data """
self.mean = self.stddev = self.maxval = self.minval = None
self.roi = self.slice = self.area_sum = None
def rebin(self, x_rebin_fact, y_rebin_fact, keep_I=True):
"""
Rebin the data and adjust dims
@param x_rebin_fact: x binning factor
@param y_rebin_fact: y binning factor
@param keep_I: shall the signal increase ?
@type x_rebin_fact: int
@type y_rebin_fact: int
@type keep_I: boolean
"""
if self.data is None:
raise Exception('Please read in the file you wish to rebin first')
if (self.dim1 % x_rebin_fact != 0) or (self.dim2 % y_rebin_fact != 0):
raise RuntimeError('image size is not divisible by rebin factor - ' + \
'skipping rebin')
else:
dataIn = self.data.astype("float64")
shapeIn = self.data.shape
shapeOut = (shapeIn[0] // y_rebin_fact, shapeIn[1] // x_rebin_fact)
binsize = y_rebin_fact * x_rebin_fact
if binsize < 50: # method faster for small binning (4x4)
out = numpy.zeros(shapeOut, dtype="float64")
for j in range(x_rebin_fact):
for i in range(y_rebin_fact):
out += dataIn[i::y_rebin_fact, j::x_rebin_fact]
else: # method faster for large binning (8x8)
temp = self.data.astype("float64")
temp.shape = (shapeOut[0], y_rebin_fact, shapeOut[1], x_rebin_fact)
out = temp.sum(axis=3).sum(axis=1)
self.resetvals()
if keep_I:
self.data = (out / (y_rebin_fact * x_rebin_fact)).astype(self.data.dtype)
else:
self.data = out.astype(self.data.dtype)
self.dim1 = self.dim1 / x_rebin_fact
self.dim2 = self.dim2 / y_rebin_fact
# update header
self.update_header()
def write(self, fname):
"""
To be overwritten - write the file
"""
raise Exception("Class has not implemented readheader method yet")
def save(self, fname):
'wrapper for write'
self.write(fname)
def readheader(self, filename):
"""
Call the _readheader function...
"""
# Override the needs asserting that all headers can be read via python modules
save_state = self._need_a_real_file , self._need_a_seek_to_read
self._need_a_real_file , self._need_a_seek_to_read = False, False
fin = self._open(filename)
self._readheader(fin)
fin.close()
self._need_a_real_file , self._need_a_seek_to_read = save_state
def _readheader(self, fik_obj):
"""
Must be overridden in classes
"""
raise Exception("Class has not implemented _readheader method yet")
def update_header(self , **kwds):
"""
update the header entries
by default pass in a dict of key, values.
"""
self.header.update(kwds)
def read(self, filename, frame=None):
"""
To be overridden - fill in self.header and self.data
"""
raise Exception("Class has not implemented read method yet")
# return self
def load(self, *arg, **kwarg):
"Wrapper for read"
return self.read(*arg, **kwarg)
def readROI(self, filename, frame=None, coords=None):
"""
Method reading Region of Interest.
This implementation is the trivial one, just doing read and crop
"""
self.read(filename, frame)
if len(coords) == 4:
self.slice = self.make_slice(coords)
elif len(coords) == 2 and isinstance(coords[0], slice) and \
isinstance(coords[1], slice):
self.slice = coords
else:
logger.warning('readROI: Unable to understand Region Of Interest: got %s', coords)
self.roi = self.data[ self.slice ]
return self.roi
def _open(self, fname, mode="rb"):
"""
Try to handle compressed files, streams, shared memory etc
Return an object which can be used for "read" and "write"
... FIXME - what about seek ?
"""
if hasattr(fname, "read") and hasattr(fname, "write"):
# It is already something we can use
if "name" in dir(fname):
self.filename = fname.name
else:
self.filename = "stream"
try:
setattr(fname, "name", self.filename)
except AttributeError:
# cStringIO
logger.warning("Unable to set filename attribute to stream (cStringIO?) of type %s" % type(fname))
return fname
fileObject = None
self.filename = fname
self.filenumber = fabioutils.extract_filenumber(fname)
if isinstance(fname, fabioutils.StringTypes):
if os.path.splitext(fname)[1] == ".gz":
fileObject = self._compressed_stream(fname,
fabioutils.COMPRESSORS['.gz'],
fabioutils.GzipFile,
mode)
elif os.path.splitext(fname)[1] == '.bz2':
fileObject = self._compressed_stream(fname,
fabioutils.COMPRESSORS['.bz2'],
fabioutils.BZ2File,
mode)
#
# Here we return the file even though it may be bzipped or gzipped
# but named incorrectly...
#
# FIXME - should we fix that or complain about the daft naming?
else:
fileObject = fabioutils.File(fname, mode)
if "name" not in dir(fileObject):
fileObject.name = fname
return fileObject
def _compressed_stream(self,
fname,
system_uncompress,
python_uncompress,
mode='rb'):
"""
Try to transparently handle gzip / bzip2 without always getting python
performance
"""
# assert that python modules are always OK based on performance benchmark
# Try to fix the way we are using them?
fobj = None
if self._need_a_real_file and mode[0] == "r":
fo = python_uncompress(fname, mode)
# problem when not administrator under certain flavors of windows
tmpfd, tmpfn = tempfile.mkstemp()
os.close(tmpfd)
fobj = fabioutils.File(tmpfn, "w+b", temporary=True)
fobj.write(fo.read())
fo.close()
fobj.seek(0)
elif self._need_a_seek_to_read and mode[0] == "r":
fo = python_uncompress(fname, mode)
fobj = fabioutils.BytesIO(fo.read(), fname, mode)
else:
fobj = python_uncompress(fname, mode)
return fobj
def convert(self, dest):
"""
Convert a fabioimage object into another fabioimage object (with possible conversions)
@param dest: destination type "EDF", "edfimage" or the class itself
@return: instance of the new class
"""
other = None
if type(dest) in fabioutils.StringTypes:
dest = dest.lower()
if dest.endswith("image"):
dest = dest[:-5]
if dest + "image" in self.registry:
other = self.factory(dest + "image")
# load modules which could be suitable:
for pref in fabioutils.FILETYPES.get(dest, []):
try:
__import__(".%simage" % pref)
other = self.factory(pref + "image")
except:
pass
else:
continue
elif isinstance(dest, self.__class__):
other = dest.__class__()
elif ("__new__" in dir(dest)) and isinstance(dest(), fabioimage):
other = dest()
else:
logger.error("Unrecognized destination format: %s " % dest)
return self
other.data = converters.convert_data(self.classname, other.classname, self.data)
other.header = converters.convert_header(self.classname, other.classname, self.header)
return other
fabioimage = FabioImage
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