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| @@ -0,0 +1,13 @@ | ||
| BasedOnStyle: WebKit | ||
| AccessModifierOffset: -4 | ||
| AlignTrailingComments: true | ||
| BreakBeforeBraces: Allman | ||
| ColumnLimit: 0 | ||
| IndentWidth: 4 | ||
| KeepEmptyLinesAtTheStartOfBlocks: false | ||
| PointerBindsToType: false | ||
| SpacesBeforeTrailingComments: 1 | ||
| TabWidth: 4 | ||
| UseTab: Never | ||
| Standard: Cpp03 | ||
|
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| # pkg-util style namespace package to allow asl package to be split over multiple locations | ||
| __path__ = __import__('pkgutil').extend_path(__path__, __name__) |
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| Original file line number | Diff line number | Diff line change |
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| #!/usr/bin/env python | ||
| # | ||
| # FSL helper functions - named fslhelpers so as not to clash with 'official' FSL python | ||
| # modules | ||
|
|
||
| import os, sys | ||
| import glob | ||
| import shutil | ||
| import shlex | ||
| import subprocess | ||
| import math | ||
| import errno | ||
|
|
||
| import nibabel as nib | ||
| import numpy as np | ||
|
|
||
| # Where to look for 'local' programs - default to dir of calling program | ||
| # This enables users to override standard FSL programs by putting their | ||
| # own copies in the same directory as the script they are calling | ||
| LOCAL_DIR = os.path.dirname(os.path.abspath(sys.argv[0])) | ||
| #print("FSLHELPERS: using local binaries dir: %s" % LOCAL_DIR) | ||
|
|
||
| def set_localdir(localdir): | ||
| global LOCAL_DIR | ||
| LOCAL_DIR = localdir | ||
|
|
||
| class Prog: | ||
| def __init__(self, cmd, localdir=""): | ||
| self.cmd = cmd | ||
|
|
||
| def _find(self): | ||
| """ | ||
| Find the program, either in the 'local' directory, or in $FSLDEVDIR/bin or $FSLDIR/bin | ||
| This is called each time the program is run so the caller can control where programs | ||
| are searched for at any time | ||
| """ | ||
| if "FSLDIR" in os.environ: | ||
| fsldir = os.environ["FSLDIR"] | ||
| else: | ||
| fsldir = LOCAL_DIR | ||
| if "FSLDEVDIR" in os.environ: | ||
| fsldevdir = os.environ["FSLDEVDIR"] | ||
| else: | ||
| fsldevdir = LOCAL_DIR | ||
|
|
||
| local_path = os.path.join(LOCAL_DIR, self.cmd) | ||
| if os.path.isfile(local_path) and os.access(local_path, os.X_OK): | ||
| return local_path | ||
| elif os.path.exists(os.path.join(fsldevdir, "bin/%s" % self.cmd)): | ||
| return os.path.join(fsldevdir, "bin/%s" % self.cmd) | ||
| elif os.path.exists(os.path.join(fsldir, "bin/%s" % self.cmd)): | ||
| return os.path.join(fsldir, "bin/%s" % self.cmd) | ||
| else: | ||
| return self.cmd | ||
|
|
||
| def run(self, args): | ||
| """ Run, writing output to stdout and returning retcode """ | ||
| cmd = self._find() | ||
| cmd_args = shlex.split(cmd + " " + args) | ||
| out = "" | ||
| #print(" ".join(cmd_args)) | ||
| p = subprocess.Popen(cmd_args, stdout=subprocess.PIPE, stderr=subprocess.STDOUT) | ||
| while 1: | ||
| retcode = p.poll() #returns None while subprocess is running | ||
| line = p.stdout.readline() | ||
| out += line | ||
| if retcode is not None: break | ||
| if retcode != 0: | ||
| raise RuntimeError(out) | ||
| else: | ||
| return out | ||
|
|
||
| class Image: | ||
| def __init__(self, fname, file_type="Image"): | ||
| if fname is None or fname == "": | ||
| raise RuntimeError("%s file not specified" % file_type) | ||
|
|
||
| self.file_type = file_type | ||
| self.base = fname.split(".", 1)[0] | ||
|
|
||
| # Try to figure out the extension | ||
| exts = ["", ".nii", ".nii.gz"] | ||
| matches = [] | ||
| for ext in exts: | ||
| if os.path.exists("%s%s" % (self.base, ext)): | ||
| matches.append(ext) | ||
|
|
||
| if len(matches) == 0: | ||
| raise RuntimeError("%s file %s not found" % (file_type, fname)) | ||
| elif len(matches) > 1: | ||
| raise RuntimeError("%s file %s is ambiguous" % (file_type, fname)) | ||
|
|
||
| self.ext = matches[0] | ||
| self.full = os.path.abspath("%s%s" % (self.base, ext)) | ||
| self.nii = nib.load(self.full) | ||
| self.shape = self.nii.shape | ||
|
|
||
| def data(self): | ||
| return self.nii.get_data() | ||
|
|
||
| def new_nifti(self, data=None): | ||
| """ Return new Nifti oject, taking header info from this image """ | ||
| if data is None: data=self.data() | ||
| nii = nib.Nifti1Image(data, self.nii.header.get_best_affine()) | ||
| nii.update_header() | ||
| return nii | ||
|
|
||
| def check_shape(self, shape=None): | ||
| if len(self.shape) != len(shape): | ||
| raise RuntimeError("%s: expected %i dims, got %i" % (self.file_type, len(shape), len(self.shape))) | ||
| if self.shape != shape: | ||
| raise RuntimeError("%s: shape (%s) does not match (%s)" % (self.file_type, str(self.shape), str(shape))) | ||
|
|
||
| maths = Prog("fslmaths") | ||
| roi = Prog("fslroi") | ||
| stats = Prog("fslstats") | ||
| merge = Prog("fslmerge") | ||
| bet = Prog("bet") | ||
| flirt = Prog("flirt") | ||
| fast = Prog("fast") | ||
|
|
||
| def imcp(src, dest): | ||
| Prog("imcp").run("%s %s" % (src, dest)) | ||
|
|
||
| def mkdir(dir, fail_if_exists=False, warn_if_exists=True): | ||
| try: | ||
| os.makedirs(dir) | ||
| except OSError as e: | ||
| if e.errno == errno.EEXIST: | ||
| if fail_if_exists: raise | ||
| elif warn_if_exists: print("WARNING: mkdir - Directory %s already exists" % dir) |
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