From a22fb99e1197042c3326585c0b2a4dd2204aa9c6 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Tue, 6 Jan 2015 13:29:50 +0000
Subject: [PATCH] All imagefile functionality is now in image module.
---
fsl/data/image.py | 163 ++++++++++++++++++++++++++++-
fsl/data/imagefile.py | 170 -------------------------------
fsl/fslview/actions/copyimage.py | 2 +-
fsl/tools/bet.py | 7 +-
4 files changed, 162 insertions(+), 180 deletions(-)
delete mode 100644 fsl/data/imagefile.py
diff --git a/fsl/data/image.py b/fsl/data/image.py
index f3ba245a8..30abf8c48 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -18,7 +18,6 @@ import numpy as np
import nibabel as nib
import props
-import fsl.data.imagefile as imagefile
import fsl.utils.transform as transform
@@ -43,6 +42,160 @@ NIFTI_XFORM_TALAIRACH = 3
NIFTI_XFORM_MNI_152 = 4
+ALLOWED_EXTENSIONS = ['.nii', '.img', '.hdr', '.nii.gz', '.img.gz']
+"""The file extensions which we understand. This list is used as the default
+if if the ``allowedExts`` parameter is not passed to any of the functions in
+this module.
+"""
+
+EXTENSION_DESCRIPTIONS = ['NIFTI1 images',
+ 'ANALYZE75 images',
+ 'NIFTI1/ANALYZE75 headers',
+ 'Compressed NIFTI1 images',
+ 'Compressed ANALYZE75/NIFTI1 images']
+"""Descriptions for each of the extensions in :data:`_allowedExts`. """
+
+
+DEFAULT_EXTENSION = '.nii.gz'
+"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
+
+
+def makeWildcard(allowedExts=None):
+ """Returns a wildcard string for use in a file dialog, to limit
+ the acceptable file types.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ if allowedExts is None:
+ allowedExts = ALLOWED_EXTENSIONS
+ descs = EXTENSION_DESCRIPTIONS
+ else:
+ descs = allowedExts
+
+ exts = ['*{}'.format(ext) for ext in allowedExts]
+
+ wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
+
+ print '|'.join(wcParts)
+ return '|'.join(wcParts)
+
+
+def isSupported(filename, allowedExts=None):
+ """
+ Returns ``True`` if the given file has a supported extension, ``False``
+ otherwise.
+
+ :arg filename: The file name to test.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
+
+ return any(map(lambda ext: filename.endswith(ext, allowedExts)))
+
+
+def removeExtension(filename, allowedExts=None):
+ """
+ Removes the extension from the given file name. Raises a :exc:`ValueError`
+ if the file has an unsupported extension.
+
+ :arg filename: The file name to strip.
+
+ :arg allowedExts: A list of strings containing the allowed file
+ extensions.
+ """
+
+ if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
+
+ # figure out the extension of the given file
+ extMatches = map(lambda ext: filename.endswith(ext), allowedExts)
+
+ # the file does not have a supported extension
+ if not any(extMatches):
+ raise ValueError('Unsupported file type')
+
+ # figure out the length of the matched extension
+ extIdx = extMatches.index(True)
+ extLen = len(allowedExts[extIdx])
+
+ # and trim it from the file name
+ return filename[:-extLen]
+
+
+def addExtension(
+ prefix,
+ mustExist=False,
+ allowedExts=None,
+ defaultExt=None):
+ """Adds a file extension to the given file ``prefix``.
+
+ If ``mustExist`` is False (the default), and the file does not already
+ have a supported extension, the default extension is appended and the new
+ file name returned. If the prefix already has a supported extension,
+ it is returned unchanged.
+
+ If ``mustExist`` is ``True``, the function checks to see if any files
+ exist that have the given prefix, and a supported file extension. A
+ :exc:`ValueError` is raised if:
+
+ - No files exist with the given prefix and a supported extension.
+ - More than one file exists with the given prefix, and a supported
+ extension.
+
+ Otherwise the full file name is returned.
+
+ :arg prefix: The file name refix to modify.
+ :arg mustExist: Whether the file must exist or not.
+ :arg allowedExts: List of allowed file extensions.
+ :arg defaultExt: Default file extension to use.
+ """
+
+ if allowedExts is None: allowedExts = ALLOWED_EXTENSIONS
+ if defaultExt is None: defaultExt = DEFAULT_EXTENSION
+
+ if not mustExist:
+
+ # the provided file name already
+ # ends with a supported extension
+ if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ return prefix
+
+ return prefix + defaultExt
+
+ # If the provided prefix already ends with a
+ # supported extension , check to see that it exists
+ if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
+ extended = [prefix]
+
+ # Otherwise, make a bunch of file names, one per
+ # supported extension, and test to see if exactly
+ # one of them exists.
+ else:
+ extended = map(lambda ext: prefix + ext, allowedExts)
+
+ exists = map(op.isfile, extended)
+
+ # Could not find any supported file
+ # with the specified prefix
+ if not any(exists):
+ raise ValueError(
+ 'Could not find a supported file with prefix {}'.format(prefix))
+
+ # Ambiguity! More than one supported
+ # file with the specified prefix
+ if len(filter(bool, exists)) > 1:
+ raise ValueError('More than one file with prefix {}'.format(prefix))
+
+ # Return the full file name of the
+ # supported file that was found
+ extIdx = exists.index(True)
+ return extended[extIdx]
+
+
def _loadImageFile(filename):
"""Given the name of an image file, loads it using nibabel.
@@ -174,7 +327,7 @@ class Image(props.HasProperties):
# The image parameter may be the name of an image file
if isinstance(image, basestring):
- nibImage, filename = _loadImageFile(imagefile.addExt(image))
+ nibImage, filename = _loadImageFile(addExtension(image))
self.nibImage = nibImage
self.imageFile = image
@@ -182,10 +335,10 @@ class Image(props.HasProperties):
# the provided file name, that means that the
# image was opened from a temporary file
if filename != image:
- self.name = op.basename(self.imageFile)
+ self.name = removeExtension(op.basename(self.imageFile))
self.tempFile = nibImage.get_filename()
else:
- self.name = op.basename(self.imageFile)
+ self.name = removeExtension(op.basename(self.imageFile))
self.saved = True
@@ -459,7 +612,7 @@ class ImageList(props.HasProperties):
# TODO wx wildcard handling is buggy,
# so i'm disabling it for now
- # wildcard = imagefile.wildcard()
+ # wildcard = wildcard()
dlg = wx.FileDialog(app.GetTopWindow(),
message='Open image file',
defaultDir=fromDir,
diff --git a/fsl/data/imagefile.py b/fsl/data/imagefile.py
deleted file mode 100644
index f11c78054..000000000
--- a/fsl/data/imagefile.py
+++ /dev/null
@@ -1,170 +0,0 @@
-#!/usr/bin/env python
-#
-# imagefile.py - Convenience functions for adding/stripping supported
-# file extensions to/from image file names.
-#
-# Author: Paul McCarthy <pauldmccarthy@gmail.com>
-#
-"""Convenience functions for adding/stripping supported
-file extensions to/from image file names.
-"""
-
-import os
-import os.path as op
-
-
-_allowedExts = ['.nii', '.img', '.hdr', '.nii.gz', '.img.gz']
-"""The file extensions which we understand. This list is used as the default
-if if the ``allowedExts`` parameter is not passed to any of the functions in
-this module.
-"""
-
-_descriptions = ['NIFTI1 images',
- 'ANALYZE75 images',
- 'NIFTI1/ANALYZE75 headers',
- 'Compressed NIFTI1 images',
- 'Compressed ANALYZE75/NIFTI1 images']
-"""Descriptions for each of the extensions in :data:`_allowedExts`. """
-
-
-_defaultExt = '.nii.gz'
-"""The default file extension (TODO read this from ``$FSLOUTPUTTYPE``)."""
-
-
-def wildcard(allowedExts=None):
- """Returns a wildcard string for use in a file dialog, to limit
- the acceptable file types.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None:
- allowedExts = _allowedExts
- descs = _descriptions
- else:
- descs = allowedExts
-
-
- exts = ['*{}'.format(ext) for ext in allowedExts]
-
- wcParts = ['|'.join((desc, ext)) for (desc, ext) in zip(descs, exts)]
-
- print '|'.join(wcParts)
- return '|'.join(wcParts)
-
-
-
-def isSupported(filename, allowedExts=None):
- """
- Returns ``True`` if the given file has a supported extension, ``False``
- otherwise.
-
- :arg filename: The file name to test.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None: allowedExts = _allowedExts
-
- return any(map(lambda ext: filename.endswith(ext, allowedExts)))
-
-
-def removeExt(filename, allowedExts=None):
- """
- Removes the extension from the given file name. Raises a :exc:`ValueError`
- if the file has an unsupported extension.
-
- :arg filename: The file name to strip.
-
- :arg allowedExts: A list of strings containing the allowed file
- extensions.
- """
-
- if allowedExts is None: allowedExts = _allowedExts
-
- # figure out the extension of the given file
- extMatches = map(lambda ext: filename.endswith(ext), allowedExts)
-
- # the file does not have a supported extension
- if not any(extMatches):
- raise ValueError('Unsupported file type')
-
- # figure out the length of the matched extension
- extIdx = extMatches.index(True)
- extLen = len(allowedExts[extIdx])
-
- # and trim it from the file name
- return filename[:-extLen]
-
-
-
-def addExt(
- prefix,
- mustExist=False,
- allowedExts=None,
- defaultExt=None):
- """Adds a file extension to the given file ``prefix``.
-
- If ``mustExist`` is False (the default), and the file does not already
- have a supported extension, the default extension is appended and the new
- file name returned. If the prefix already has a supported extension,
- it is returned unchanged.
-
- If ``mustExist`` is ``True``, the function checks to see if any files
- exist that have the given prefix, and a supported file extension. A
- :exc:`ValueError` is raised if:
-
- - No files exist with the given prefix and a supported extension.
- - More than one file exists with the given prefix, and a supported
- extension.
-
- Otherwise the full file name is returned.
-
- :arg prefix: The file name refix to modify.
- :arg mustExist: Whether the file must exist or not.
- :arg allowedExts: List of allowed file extensions.
- :arg defaultExt: Default file extension to use.
- """
-
- if allowedExts is None: allowedExts = _allowedExts
- if defaultExt is None: defaultExt = _defaultExt
-
- if not mustExist:
-
- # the provided file name already
- # ends with a supported extension
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
- return prefix
-
- return prefix + defaultExt
-
- # If the provided prefix already ends with a
- # supported extension , check to see that it exists
- if any(map(lambda ext: prefix.endswith(ext), allowedExts)):
- extended = [prefix]
-
- # Otherwise, make a bunch of file names, one per
- # supported extension, and test to see if exactly
- # one of them exists.
- else:
- extended = map(lambda ext: prefix + ext, allowedExts)
-
- exists = map(op.isfile, extended)
-
- # Could not find any supported file
- # with the specified prefix
- if not any(exists):
- raise ValueError(
- 'Could not find a supported file with prefix {}'.format(prefix))
-
- # Ambiguity! More than one supported
- # file with the specified prefix
- if len(filter(bool, exists)) > 1:
- raise ValueError('More than one file with prefix {}'.format(prefix))
-
- # Return the full file name of the
- # supported file that was found
- extIdx = exists.index(True)
- return extended[extIdx]
diff --git a/fsl/fslview/actions/copyimage.py b/fsl/fslview/actions/copyimage.py
index e27994643..e641ed164 100644
--- a/fsl/fslview/actions/copyimage.py
+++ b/fsl/fslview/actions/copyimage.py
@@ -25,7 +25,7 @@ class CopyImageAction(actions.Action):
data = np.copy(image.data)
xform = image.voxToWorldMat
- name = '{} copy'.format(image.name)
+ name = '{}_copy'.format(image.name)
copy = fslimage.Image(data, xform, name)
self._imageList.insert(imageIdx + 1, copy)
diff --git a/fsl/tools/bet.py b/fsl/tools/bet.py
index aad1f5996..85af2b83b 100644
--- a/fsl/tools/bet.py
+++ b/fsl/tools/bet.py
@@ -9,7 +9,6 @@ from collections import OrderedDict
import props
-import fsl.data.imagefile as imagefile
import fsl.data.image as fslimage
import fsl.utils.transform as transform
import fsl.fslview.displaycontext as displaycontext
@@ -34,12 +33,12 @@ class Options(props.HasProperties):
inputImage = props.FilePath(
exists=True,
- suffixes=imagefile._allowedExts,
+ suffixes=fslimage.ALLOWED_EXTENSIONS,
required=True)
outputImage = props.FilePath(required=True)
t2Image = props.FilePath(
exists=True,
- suffixes=imagefile._allowedExts,
+ suffixes=fslimage.ALLOWED_EXTENSIONS,
required=lambda i: i.runChoice == '-A2')
runChoice = props.Choice(runChoices)
@@ -66,7 +65,7 @@ class Options(props.HasProperties):
"""
if not valid: return
- value = imagefile.removeExt(value)
+ value = fslimage.removeExtension(value)
self.outputImage = value + '_brain'
--
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