# -*- coding: utf-8 -*-
#
# Copyright © 2009-2012 CEA
# Pierre Raybaut
# Licensed under the terms of the CECILL License
# (see guiqwt/__init__.py for details)
# pylint: disable=C0103
"""
guiqwt.io
---------
The `io` module provides input/output helper functions:
* :py:func:`guiqwt.io.imread`: load an image (.png, .tiff,
.dicom, etc.) and return its data as a NumPy array
* :py:func:`guiqwt.io.imwrite`: save an array to an image file
* :py:func:`guiqwt.io.load_items`: load plot items from HDF5
* :py:func:`guiqwt.io.save_items`: save plot items to HDF5
Reference
~~~~~~~~~
.. autofunction:: imread
.. autofunction:: imwrite
.. autofunction:: load_items
.. autofunction:: save_items
"""
import sys
import re
import os.path as osp
import numpy as np
# Local imports
from guiqwt.config import _
def scale_data_to_dtype(data, dtype):
"""Scale array `data` to fit datatype `dtype` dynamic range
WARNING: modifies data in place"""
info = np.iinfo(dtype)
dmin = data.min()
dmax = data.max()
data -= dmin
data *= float(info.max - info.min) / (dmax - dmin)
data += float(info.min)
return np.array(data, dtype)
def eliminate_outliers(data, percent=2.0, bins=256):
"""Eliminate data histogram outliers"""
hist, bin_edges = np.histogram(data, bins)
from guiqwt.histogram import hist_range_threshold
vmin, vmax = hist_range_threshold(hist, bin_edges, percent)
return data.clip(vmin, vmax)
# ===============================================================================
# I/O File type definitions
# ===============================================================================
class FileType(object):
"""Filetype object:
* `name` : description of filetype,
* `read_func`, `write_func` : I/O callbacks,
* `extensions`: filename extensions (with a dot!) or filenames,
(list, tuple or space-separated string)
* `data_types`: supported data types"""
def __init__(
self,
name,
extensions,
read_func=None,
write_func=None,
data_types=None,
requires_template=False,
):
self.name = name
if isinstance(extensions, str):
extensions = extensions.split()
self.extensions = [osp.splitext(" " + ext)[1] for ext in extensions]
self.read_func = read_func
self.write_func = write_func
self.data_types = data_types
self.requires_template = requires_template
def matches(self, action, dtype, template):
"""Return True if file type matches passed data type and template
(or if dtype is None)"""
assert action in ("load", "save")
matches = dtype is None or self.data_types is None or dtype in self.data_types
if action == "save" and self.requires_template:
matches = matches and template is not None
return matches
@property
def wcards(self):
return "*" + (" *".join(self.extensions))
def filters(self, action, dtype, template):
assert action in ("load", "save")
if self.matches(action, dtype, template):
return "\n%s (%s)" % (self.name, self.wcards)
else:
return ""
class ImageIOHandler(object):
"""I/O handler: regroup all FileType objects"""
def __init__(self):
self.filetypes = []
def allfilters(self, action, dtype, template):
wcards = " ".join(
[
ftype.wcards
for ftype in self.filetypes
if ftype.matches(action, dtype, template)
]
)
return "%s (%s)" % (_("All supported files"), wcards)
def get_filters(self, action, dtype=None, template=None):
"""Return file type filters for `action` (string: 'save' or 'load'),
`dtype` data type (None: all data types), and `template` (True if save
function requires a template (e.g. DICOM files), False otherwise)"""
filters = self.allfilters(action, dtype, template)
for ftype in self.filetypes:
filters += ftype.filters(action, dtype, template)
return filters
def add(
self,
name,
extensions,
read_func=None,
write_func=None,
import_func=None,
data_types=None,
requires_template=None,
):
if import_func is not None:
try:
import_func()
except ImportError:
return
assert read_func is not None or write_func is not None
ftype = FileType(
name,
extensions,
read_func=read_func,
write_func=write_func,
data_types=data_types,
requires_template=requires_template,
)
self.filetypes.append(ftype)
def _get_filetype(self, ext):
"""Return FileType object associated to file extension `ext`"""
for ftype in self.filetypes:
if ext.lower() in ftype.extensions:
return ftype
else:
raise RuntimeError("Unsupported file type: '%s'" % ext)
def get_readfunc(self, ext):
"""Return read function associated to file extension `ext`"""
ftype = self._get_filetype(ext)
if ftype.read_func is None:
raise RuntimeError("Unsupported file type (read): '%s'" % ext)
else:
return ftype.read_func
def get_writefunc(self, ext):
"""Return read function associated to file extension `ext`"""
ftype = self._get_filetype(ext)
if ftype.write_func is None:
raise RuntimeError("Unsupported file type (write): '%s'" % ext)
else:
return ftype.write_func
iohandler = ImageIOHandler()
# ==============================================================================
# tifffile-based Private I/O functions
# ==============================================================================
def _imread_tiff(filename):
"""Open a TIFF image and return a NumPy array"""
try:
import tifffile
return tifffile.imread(filename)
except ImportError:
return _imread_pil(filename)
def _imwrite_tiff(filename, arr):
"""Save a NumPy array to a TIFF file"""
try:
import tifffile
return tifffile.imwrite(filename, arr)
except ImportError:
return _imwrite_pil(filename, arr)
# ==============================================================================
# PIL-based Private I/O functions
# ==============================================================================
if sys.byteorder == "little":
_ENDIAN = "<"
else:
_ENDIAN = ">"
DTYPES = {
"1": ("|b1", None),
"L": ("|u1", None),
"I": ("%si4" % _ENDIAN, None),
"F": ("%sf4" % _ENDIAN, None),
"I;16": ("%su2" % _ENDIAN, None),
"I;16B": ("%su2" % _ENDIAN, None),
"I;16S": ("%si2" % _ENDIAN, None),
"P": ("|u1", None),
"RGB": ("|u1", 3),
"RGBX": ("|u1", 4),
"RGBA": ("|u1", 4),
"CMYK": ("|u1", 4),
"YCbCr": ("|u1", 4),
}
def _imread_pil(filename, to_grayscale=False):
"""Open image with PIL and return a NumPy array"""
import PIL.Image
import PIL.TiffImagePlugin # py2exe
PIL.TiffImagePlugin.OPEN_INFO[(PIL.TiffImagePlugin.II, 0, 1, 1, (16,), ())] = (
"I;16",
"I;16",
)
img = PIL.Image.open(filename)
if img.mode in ("CMYK", "YCbCr"):
# Converting to RGB
img = img.convert("RGB")
if to_grayscale and img.mode in ("RGB", "RGBA", "RGBX"):
# Converting to grayscale
img = img.convert("L")
elif "A" in img.mode or (img.mode == "P" and "transparency" in img.info):
img = img.convert("RGBA")
elif img.mode == "P":
img = img.convert("RGB")
try:
dtype, extra = DTYPES[img.mode]
except KeyError:
raise RuntimeError("%s mode is not supported" % img.mode)
shape = (img.size[1], img.size[0])
if extra is not None:
shape += (extra,)
try:
return np.array(img, dtype=np.dtype(dtype)).reshape(shape)
except SystemError:
return np.array(img.getdata(), dtype=np.dtype(dtype)).reshape(shape)
def _imwrite_pil(filename, arr):
"""Write `arr` NumPy array to `filename` using PIL"""
import PIL.Image
import PIL.TiffImagePlugin # py2exe
for mode, (dtype_str, extra) in list(DTYPES.items()):
if dtype_str == arr.dtype.str:
if extra is None: # mode for grayscale images
if len(arr.shape[2:]) > 0:
continue # not suitable for RGB(A) images
else:
break # this is it!
else: # mode for RGB(A) images
if len(arr.shape[2:]) == 0:
continue # not suitable for grayscale images
elif arr.shape[-1] == extra:
break # this is it!
else:
raise RuntimeError("Cannot determine PIL data type")
img = PIL.Image.fromarray(arr, mode)
img.save(filename)
# ==============================================================================
# DICOM Private I/O functions
# ==============================================================================
def _import_dcm():
"""DICOM Import function (checking for required libraries):
DICOM support requires library `pydicom`"""
import logging
logger = logging.getLogger("pydicom")
logger.setLevel(logging.CRITICAL)
from pydicom import dicomio # analysis:ignore
logger.setLevel(logging.WARNING)
def _imread_dcm(filename):
"""Open DICOM image with pydicom and return a NumPy array"""
from pydicom import dicomio
dcm = dicomio.read_file(filename, force=True)
# **********************************************************************
# The following is necessary until pydicom numpy support is improved:
# (after that, a simple: 'arr = dcm.PixelArray' will work the same)
format_str = "%sint%s" % (("u", "")[dcm.PixelRepresentation], dcm.BitsAllocated)
try:
dtype = np.dtype(format_str)
except TypeError:
raise TypeError(
"Data type not understood by NumPy: "
"PixelRepresentation=%d, BitsAllocated=%d"
% (dcm.PixelRepresentation, dcm.BitsAllocated)
)
arr = np.fromstring(dcm.PixelData, dtype)
try:
# pydicom 0.9.3:
dcm_is_little_endian = dcm.isLittleEndian
except AttributeError:
# pydicom 0.9.4:
dcm_is_little_endian = dcm.is_little_endian
if dcm_is_little_endian != (sys.byteorder == "little"):
arr.byteswap(True)
spp = getattr(dcm, "SamplesperPixel", 1)
if hasattr(dcm, "NumberofFrames") and dcm.NumberofFrames > 1:
if spp > 1:
arr = arr.reshape(spp, dcm.NumberofFrames, dcm.Rows, dcm.Columns)
else:
arr = arr.reshape(dcm.NumberofFrames, dcm.Rows, dcm.Columns)
else:
if spp > 1:
if dcm.BitsAllocated == 8:
arr = arr.reshape(spp, dcm.Rows, dcm.Columns)
else:
raise NotImplementedError(
"This code only handles "
"SamplesPerPixel > 1 if Bits Allocated = 8"
)
else:
arr = arr.reshape(dcm.Rows, dcm.Columns)
# **********************************************************************
return arr
def _imwrite_dcm(filename, arr, template=None):
"""Save a numpy array `arr` into a DICOM image file `filename`
based on DICOM structure `template`"""
# Note: due to IOHandler formalism, `template` has to be a keyword argument
assert template is not None, (
"The `template` keyword argument is required to save DICOM files\n"
"(that is the template DICOM structure object)"
)
infos = np.iinfo(arr.dtype)
template.BitsAllocated = infos.bits
template.BitsStored = infos.bits
template.HighBit = infos.bits - 1
template.PixelRepresentation = ("u", "i").index(infos.kind)
data_vr = ("US", "SS")[template.PixelRepresentation]
template.Rows = arr.shape[0]
template.Columns = arr.shape[1]
template.SmallestImagePixelValue = int(arr.min())
template[0x00280106].VR = data_vr
template.LargestImagePixelValue = int(arr.max())
template[0x00280107].VR = data_vr
if not template.PhotometricInterpretation.startswith("MONOCHROME"):
template.PhotometricInterpretation = "MONOCHROME1"
template.PixelData = arr.tostring()
template[0x7FE00010].VR = "OB"
template.save_as(filename)
# ==============================================================================
# Text files Private I/O functions
# ==============================================================================
def _imread_txt(filename):
"""Open text file image and return a NumPy array"""
for delimiter in ("\t", ",", " ", ";"):
try:
return np.loadtxt(filename, delimiter=delimiter)
except ValueError:
continue
else:
raise
def _imwrite_txt(filename, arr):
"""Write `arr` NumPy array to text file `filename`"""
if arr.dtype in (np.int8, np.uint8, np.int16, np.uint16, np.int32, np.uint32):
fmt = "%d"
else:
fmt = "%.18e"
ext = osp.splitext(filename)[1]
if ext.lower() in (".txt", ".asc", ""):
np.savetxt(filename, arr, fmt=fmt)
elif ext.lower() == ".csv":
np.savetxt(filename, arr, fmt=fmt, delimiter=",")
# ==============================================================================
# Registering I/O functions
# ==============================================================================
iohandler.add(
_("PNG files"),
"*.png",
read_func=_imread_pil,
write_func=_imwrite_pil,
data_types=(np.uint8, np.uint16),
)
iohandler.add(
_("TIFF files"), "*.tif *.tiff", read_func=_imread_tiff, write_func=_imwrite_tiff
)
iohandler.add(
_("8-bit images"),
"*.jpg *.gif",
read_func=_imread_pil,
write_func=_imwrite_pil,
data_types=(np.uint8,),
)
iohandler.add(_("NumPy arrays"), "*.npy", read_func=np.load, write_func=np.save)
iohandler.add(
_("Text files"), "*.txt *.csv *.asc", read_func=_imread_txt, write_func=_imwrite_txt
)
iohandler.add(
_("DICOM files"),
"*.dcm",
read_func=_imread_dcm,
write_func=_imwrite_dcm,
import_func=_import_dcm,
data_types=(np.int8, np.uint8, np.int16, np.uint16),
requires_template=True,
)
# ==============================================================================
# Generic image read/write functions
# ==============================================================================
[docs]def imread(fname, ext=None, to_grayscale=False):
"""Return a NumPy array from an image filename `fname`.
If `to_grayscale` is True, convert RGB images to grayscale
The `ext` (optional) argument is a string that specifies the file extension
which defines the input format: when not specified, the input format is
guessed from filename."""
if ext is None:
_base, ext = osp.splitext(fname)
arr = iohandler.get_readfunc(ext)(fname)
if to_grayscale and arr.ndim == 3:
# Converting to grayscale
return arr[..., :4].mean(axis=2)
else:
return arr
[docs]def imwrite(fname, arr, ext=None, dtype=None, max_range=None, **kwargs):
"""Save a NumPy array to an image filename `fname`.
If `to_grayscale` is True, convert RGB images to grayscale
The `ext` (optional) argument is a string that specifies the file extension
which defines the input format: when not specified, the input format is
guessed from filename.
If `max_range` is True, array data is scaled to fit the `dtype` (or data
type itself if `dtype` is None) dynamic range
Warning: option `max_range` changes data in place"""
if ext is None:
_base, ext = osp.splitext(fname)
if max_range:
arr = scale_data_to_dtype(arr, arr.dtype if dtype is None else dtype)
iohandler.get_writefunc(ext)(fname, arr, **kwargs)
# ==============================================================================
# Deprecated functions
# ==============================================================================
def imagefile_to_array(filename, to_grayscale=False):
"""
Return a NumPy array from an image file `filename`
If `to_grayscale` is True, convert RGB images to grayscale
"""
print("io.imagefile_to_array is deprecated: use io.imread instead", file=sys.stderr)
return imread(filename, to_grayscale=to_grayscale)
def array_to_imagefile(arr, filename, mode=None, max_range=False):
"""
Save a numpy array `arr` into an image file `filename`
Warning: option 'max_range' changes data in place
"""
print(
"io.array_to_imagefile is deprecated: use io.imwrite instead", file=sys.stderr
)
return imwrite(filename, arr, mode=mode, max_range=max_range)
# ==============================================================================
# guiqwt plot items I/O
# ==============================================================================
SERIALIZABLE_ITEMS = []
ITEM_MODULES = {}
def register_serializable_items(modname, classnames):
"""Register serializable item from module name and class name"""
global SERIALIZABLE_ITEMS, ITEM_MODULES
SERIALIZABLE_ITEMS += classnames
ITEM_MODULES[modname] = ITEM_MODULES.setdefault(modname, []) + classnames
# Curves
register_serializable_items(
"guiqwt.curve", ["CurveItem", "PolygonMapItem", "ErrorBarCurveItem"]
)
# Images
register_serializable_items(
"guiqwt.image",
[
"RawImageItem",
"ImageItem",
"TrImageItem",
"XYImageItem",
"RGBImageItem",
"MaskedImageItem",
],
)
# Shapes
register_serializable_items(
"guiqwt.shapes",
[
"Marker",
"PolygonShape",
"PointShape",
"SegmentShape",
"RectangleShape",
"ObliqueRectangleShape",
"EllipseShape",
"Axes",
],
)
# Annotations
register_serializable_items(
"guiqwt.annotations",
[
"AnnotatedPoint",
"AnnotatedSegment",
"AnnotatedRectangle",
"AnnotatedObliqueRectangle",
"AnnotatedEllipse",
"AnnotatedCircle",
],
)
# Labels
register_serializable_items(
"guiqwt.label", ["LabelItem", "LegendBoxItem", "SelectedLegendBoxItem"]
)
def item_class_from_name(name):
"""Return plot item class from class name"""
global SERIALIZABLE_ITEMS, ITEM_MODULES
assert name in SERIALIZABLE_ITEMS, "Unknown class %r" % name
for modname, names in list(ITEM_MODULES.items()):
if name in names:
return getattr(__import__(modname, fromlist=[name]), name)
def item_name_from_object(obj):
"""Return plot item class name from instance"""
return obj.__class__.__name__
def save_item(writer, group_name, item):
"""Save plot item to HDF5 group"""
with writer.group(group_name):
if item is None:
writer.write_none()
else:
item.serialize(writer)
with writer.group("item_class_name"):
writer.write_str(item_name_from_object(item))
def load_item(reader, group_name):
"""Load plot item from HDF5 group"""
with reader.group(group_name):
with reader.group("item_class_name"):
try:
klass_name = reader.read_str()
except ValueError:
# None was saved instead of a real item
return
klass = item_class_from_name(klass_name)
item = klass()
item.deserialize(reader)
return item
[docs]def save_items(writer, items):
"""Save items to HDF5 file:
* writer: :py:class:`guidata.hdf5io.HDF5Writer` object
* items: serializable plot items"""
counts = {}
names = []
def _get_name(item):
basename = item_name_from_object(item)
count = counts[basename] = counts.setdefault(basename, 0) + 1
name = "%s_%03d" % (basename, count)
names.append(name.encode("utf-8"))
return name
for item in items:
with writer.group(_get_name(item)):
item.serialize(writer)
with writer.group("plot_items"):
writer.write_sequence(names)
[docs]def load_items(reader):
"""Load items from HDF5 file:
* reader: :py:class:`guidata.hdf5io.HDF5Reader` object"""
with reader.group("plot_items"):
names = reader.read_sequence()
items = []
for name in names:
try:
name_str = name.decode()
except AttributeError:
name_str = name
klass_name = re.match(r"([A-Z]+[A-Za-z0-9\_]*)\_([0-9]*)", name_str).groups()[0]
klass = item_class_from_name(klass_name)
item = klass()
with reader.group(name):
item.deserialize(reader)
items.append(item)
return items
if __name__ == "__main__":
# Test if items can all be constructed from their Python module
for name in SERIALIZABLE_ITEMS:
print(name, "-->", item_class_from_name(name))
