From c3996827efc002d7551f85a162294c25ea56cff8 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 24 Jun 2019 17:19:18 +0930
Subject: [PATCH] ENH: New Bitmap class, for loading bitmap images
---
fsl/data/bitmap.py | 155 +++++++++++++++++++++++++++++++++++++++++++++
fsl/data/utils.py | 3 +
2 files changed, 158 insertions(+)
create mode 100644 fsl/data/bitmap.py
diff --git a/fsl/data/bitmap.py b/fsl/data/bitmap.py
new file mode 100644
index 000000000..1f6641716
--- /dev/null
+++ b/fsl/data/bitmap.py
@@ -0,0 +1,155 @@
+#!/usr/bin/env python
+#
+# bitmap.py - The Bitmap class
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+"""This module contains the :class:`Bitmap` class, for loading bitmap image
+files.
+"""
+
+
+import os.path as op
+import logging
+import six
+
+import numpy as np
+import PIL.Image as Image
+
+from . import image as fslimage
+
+
+log = logging.getLogger(__name__)
+
+
+BITMAP_EXTENSIONS = ['.bmp', '.png', '.jpg', '.jpeg',
+ '.tif', '.tiff', '.gif', '.rgba']
+"""File extensions we understand. """
+
+
+BITMAP_DESCRIPTIONS = [
+ 'Bitmap',
+ 'Portable Network Graphics',
+ 'JPEG',
+ 'JPEG',
+ 'TIFF',
+ 'TIFF',
+ 'Graphics Interchange Format',
+ 'Raw RGBA']
+"""A description for each :attr:`BITMAP_EXTENSION`. """
+
+
+class Bitmap(object):
+ """The ``Bitmap`` class can be used to load a bitmap image. The
+ :meth:`asImage` method will convert the bitmap into an :class:`.Image`
+ instance.
+ """
+
+ def __init__(self, bmp):
+ """Create a ``Bitmap``.
+
+ :arg bmp: File name of an image, or a ``numpy`` array containing image
+ data.
+ """
+
+ if isinstance(bmp, six.string_types):
+ source = bmp
+ data = np.array(Image.open(source))
+
+ elif isinstance(bmp, np.ndarray):
+ source = 'array'
+ data = np.copy(bmp)
+
+ else:
+ raise ValueError('unknown bitmap: {}'.format(bmp))
+
+ # Make the array (w, h, c)
+ data = data.transpose((1, 0, 2))
+ w, h = data.shape[:2]
+ data = np.array(data, dtype=np.uint8, order='C')
+
+ self.__data = data
+ self.__dataSource = source
+ self.__name = op.basename(source)
+
+
+ def __hash__(self):
+ """Returns a number which uniquely idenfities this ``Bitmap`` instance
+ (the result of ``id(self)``).
+ """
+ return id(self)
+
+
+ def __str__(self):
+ """Return a string representation of this ``Bitmap`` instance."""
+ return '{}({}, {})'.format(self.__class__.__name__,
+ self.dataSource,
+ self.shape)
+
+
+ def __repr__(self):
+ """See the :meth:`__str__` method. """
+ return self.__str__()
+
+
+ @property
+ def name(self):
+ """Returns the name of this ``Bitmap``, typically the base name of the
+ file.
+ """
+ return self.__name
+
+
+ @property
+ def dataSource(self):
+ """Returns the bitmap data source - typically the file name. """
+ return self.__dataSource
+
+
+ @property
+ def data(self):
+ """Convenience method which returns the bitmap data as a ``(w, h, c)``
+ array, where ``c`` is either 3 or 4.
+ """
+ return self.__data
+
+
+ @property
+ def shape(self):
+ """Returns the bitmap shape - ``(width, height, nchannels)``. """
+ return self.__data.shape
+
+
+ def asImage(self):
+ """Convert this ``Bitmap`` into an :class:`.Image` instance. """
+
+ width, height, nchannels = self.shape
+
+ if nchannels == 1:
+ dtype = np.uint8
+
+
+ elif nchannels == 3:
+ dtype = np.dtype([('R', 'uint8'),
+ ('G', 'uint8'),
+ ('B', 'uint8')])
+
+ elif nchannels == 4:
+ dtype = np.dtype([('R', 'uint8'),
+ ('G', 'uint8'),
+ ('B', 'uint8'),
+ ('A', 'uint8')])
+
+ else:
+ raise ValueError('Cannot convert bitmap with {} '
+ 'channels into nifti image'.format(nchannels))
+
+ if nchannels == 1:
+ data = self.data.reshape((width, height))
+
+ else:
+ data = np.zeros((width, height), dtype=dtype)
+ for ch, ci in enumerate(dtype.names):
+ data[ch] = self.data[..., ci]
+
+ return fslimage.Image(data, np.eye(4))
diff --git a/fsl/data/utils.py b/fsl/data/utils.py
index 13aae313b..bc2c1e334 100644
--- a/fsl/data/utils.py
+++ b/fsl/data/utils.py
@@ -27,6 +27,7 @@ def guessType(path):
import fsl.data.gifti as fslgifti
import fsl.data.freesurfer as fslfs
import fsl.data.mghimage as fslmgh
+ import fsl.data.bitmap as fslbmp
import fsl.data.featimage as featimage
import fsl.data.melodicimage as melimage
import fsl.data.dtifit as dtifit
@@ -56,6 +57,8 @@ def guessType(path):
return fslfs.FreesurferMesh, path
elif fslpath.hasExt(path, fslmgh.ALLOWED_EXTENSIONS):
return fslmgh.MGHImage, path
+ elif fslpath.hasExt(path, fslbmp.BITMAP_EXTENSIONS):
+ return fslbmp.Bitmap, path
# Other specialised image types
elif melanalysis .isMelodicImage(path):
--
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