<filename>tests/test_immv_imcp.py
#!/usr/bin/env python
#
# test_immv_imcp.py -
#
# Author: <NAME> <<EMAIL>>
#

from __future__ import print_function



import os.path    as op
import               os
import               shutil
import               tempfile

import numpy as np
import nibabel as nib

import fsl.utils.imcp        as imcp
import fsl.data.image        as fslimage

from . import make_random_image
from . import make_dummy_file
from . import looks_like_image


real_print = print

def print(*args, **kwargs):
    pass


def makeImage(filename):
    return hash(np.asanyarray(make_random_image(filename).dataobj).tobytes())


def checkImageHash(filename, datahash):
    """Checks that the given NIFTI image matches the given hash.
    """

    img = nib.load(filename)
    assert hash(np.asanyarray(img.dataobj).tobytes()) == datahash


def checkFilesToExpect(files, outdir, outputType, datahashes):

    exts = {
        'NIFTI'      : ['.nii'],
        'NIFTI_PAIR' : ['.hdr', '.img'],
        'NIFTI_GZ'   : ['.nii.gz'],
        ''           : ['.nii.gz'],
    }.get(outputType, None)

    allFiles = []

    if isinstance(files, str):
        files = files.split()

    for f in files:

        f, fe = fslimage.splitExt(f)
        fexts = exts

        if fexts is None:
            fexts = {
                '.img'    : ['.hdr', '.img'],
                '.hdr'    : ['.hdr', '.img'],
                '.nii'    : ['.nii'],
                '.nii.gz' : ['.nii.gz']
            }.get(fe, [])
        # filename already has a different extension
        elif fe != '' and fe not in fexts:
            fexts = [fe]

        for e in fexts:

            expected = op.join(outdir, f + e)

            allFiles.append(expected)

            print('  ', expected)

            assert op.exists(expected)

    allThatExist = os.listdir(outdir)
    allThatExist = [f for f in allThatExist if op.isfile(op.join(outdir, f))]

    assert len(allThatExist) == len(allFiles)

    for i, f in enumerate(files):
        f = fslimage.addExt(op.join(outdir, f), mustExist=True)

        if isinstance(datahashes, list):
            if len(datahashes) > len(files):
                diff = len(datahashes) - len(files)
                h    = datahashes[i + diff]

            else:
                h = datahashes[i]
        else:
            h = datahashes[op.basename(f)]

        checkImageHash(f, h)


def test_imcp_shouldPass(move=False):


    #
    # if not useDefaultExt:
    #
    #      imcp src.img dest     -> dest.img
    #      imcp src.img dest.nii -> dest.nii
    #
    # if defaultExt:
    #      imgp src.img dest     -> dest.nii.gz
    #      imgp src.img dest.nii -> dest.nii.gz

    #
    # (files_to_create,
    #    [( imcp_args, files_which_should_exist),
    #     ...
    #    ]
    # )
    shouldPass = [
        ('file.img', [
            ('file     file',     'file.img'),
            ('file     file.img', 'file.img'),
            ('file     file.hdr', 'file.img'),
            ('file     .',        'file.img'),
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
        ]),

        ('file.img file.blob', [
            ('file     file',     'file.img'),
            ('file     file.img', 'file.img'),
            ('file     file.hdr', 'file.img'),
            ('file     .',        'file.img'),
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
        ]),


        ('file.img file.nii', [
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),

            # TODO both img/nii files
        ]),


        ('file.nii', [
            ('file     file',     'file.nii'),
            ('file     file.nii', 'file.nii'),
            ('file     .',        'file.nii'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),
            ('file.nii .',        'file.nii'),
        ]),

        ('file.nii.gz', [
            ('file        file',        'file.nii.gz'),
            ('file        file.nii.gz', 'file.nii.gz'),
            ('file        .',           'file.nii.gz'),
            ('file.nii.gz file',        'file.nii.gz'),
            ('file.nii.gz file.nii.gz', 'file.nii.gz'),
            ('file.nii.gz .',           'file.nii.gz'),
        ]),


        ('file.nii file.blob', [
            ('file     file',     'file.nii'),
            ('file     file.nii', 'file.nii'),
            ('file     .',        'file.nii'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),
            ('file.nii .',        'file.nii'),
        ]),


        ('file.nii file.nii.gz', [
            ('file.nii    file',        'file.nii'),
            ('file.nii    file.nii',    'file.nii'),
            ('file.nii    .',           'file.nii'),
            ('file.nii.gz file',        'file.nii.gz'),
            ('file.nii.gz file.nii.gz', 'file.nii.gz'),
            ('file.nii.gz .',           'file.nii.gz'),

            # TODO both
        ]),

        ('file.img file.nii file.nii.gz', [
            ('file.img file.nii file.nii.gz .', 'file.img file.nii file.nii.gz'),
            ('file.img                      .', 'file.img'),
            ('file.img                      .', 'file.img'),
            ('file.nii                      .', 'file.nii'),
            ('file.nii file.nii.gz          .', 'file.nii file.nii.gz'),
        ]),


        ('001.img 002.img 003.img', [

            ('001     002     003     .', '001.img 002.img 003.img'),
            ('001.img 002.img 003.img .', '001.img 002.img 003.img'),
            ('001.hdr 002.hdr 003.hdr .', '001.img 002.img 003.img'),

            ('001.img 002     003     .', '001.img 002.img 003.img'),
            ('001.hdr 002     003     .', '001.img 002.img 003.img'),

            ('001.img 002.hdr 003.img .', '001.img 002.img 003.img'),
            ('001.hdr 002.img 003.hdr .', '001.img 002.img 003.img'),

            ('001     003             .', '001.img 003.img'),
            ('001.img 003.img         .', '001.img 003.img'),
            ('001.hdr 003.hdr         .', '001.img 003.img'),

            ('001.img 003             .', '001.img 003.img'),
            ('001.hdr 003             .', '001.img 003.img'),

            ('001.img 003.img         .', '001.img 003.img'),
            ('001.hdr 003.hdr         .', '001.img 003.img'),
        ]),
    ]


    indir  = tempfile.mkdtemp()
    outdir = tempfile.mkdtemp()

    try:

        for files_to_create, tests in shouldPass:

            files_to_create = files_to_create.split()

            for imcp_args, should_exist in tests:

                should_exist    = should_exist.split()
                imcp_args       = imcp_args.split()
                imcp_srcs       = imcp_args[:-1]
                imcp_dest       = imcp_args[ -1]

                hashes = {}
                for fn in files_to_create:
                    if looks_like_image(fn):
                        hashes[fn] = makeImage(op.join(indir, fn))
                    else:
                        hashes[fn] = make_dummy_file(op.join(indir, fn))

                print()
                print('files_to_create: ', files_to_create)
                print('imcp_srcs:       ', imcp_srcs)
                print('imcp_dest:       ', imcp_dest)
                print('should_exist:    ', should_exist)
                print('indir:           ', os.listdir(indir))

                for src in imcp_srcs:

                    print('  src: {}'.format(src))

                    src = op.join(indir, src)

                    if move: imcp.immv(src, op.join(outdir, imcp_dest), overwrite=True)
                    else:    imcp.imcp(src, op.join(outdir, imcp_dest), overwrite=True)


                print('indir after:     ', os.listdir(indir))
                print('outdir after:    ', os.listdir(outdir))

                # check file contents
                checkFilesToExpect(should_exist,
                                   outdir,
                                   None,
                                   hashes)

                # If move, check that
                # input files are gone
                if move:
                    for f in should_exist:
                         assert not op.exists(op.join(indir, f))

                for f in os.listdir(indir):
                    try:    os.remove(op.join(indir,  f))
                    except: pass

                for f in os.listdir(outdir):
                    os.remove(op.join(outdir, f))


    finally:
        shutil.rmtree(indir)
        shutil.rmtree(outdir)


def test_immv_shouldPass():
    test_imcp_shouldPass(move=True)

<filename>tests/test_immv_imcp.py
#!/usr/bin/env python
#
# test_immv_imcp.py -
#
# Author: <NAME> <<EMAIL>>
#

from __future__ import print_function



import os.path    as op
import               os
import               shutil
import               tempfile

import numpy as np
import nibabel as nib

import fsl.utils.imcp        as imcp
import fsl.data.image        as fslimage

from . import make_random_image
from . import make_dummy_file
from . import looks_like_image


real_print = print

def print(*args, **kwargs):
    pass


def makeImage(filename):
    return hash(np.asanyarray(make_random_image(filename).dataobj).tobytes())


def checkImageHash(filename, datahash):
    """Checks that the given NIFTI image matches the given hash.
    """

    img = nib.load(filename)
    assert hash(np.asanyarray(img.dataobj).tobytes()) == datahash


def checkFilesToExpect(files, outdir, outputType, datahashes):

    exts = {
        'NIFTI'      : ['.nii'],
        'NIFTI_PAIR' : ['.hdr', '.img'],
        'NIFTI_GZ'   : ['.nii.gz'],
        ''           : ['.nii.gz'],
    }.get(outputType, None)

    allFiles = []

    if isinstance(files, str):
        files = files.split()

    for f in files:

        f, fe = fslimage.splitExt(f)
        fexts = exts

        if fexts is None:
            fexts = {
                '.img'    : ['.hdr', '.img'],
                '.hdr'    : ['.hdr', '.img'],
                '.nii'    : ['.nii'],
                '.nii.gz' : ['.nii.gz']
            }.get(fe, [])
        # filename already has a different extension
        elif fe != '' and fe not in fexts:
            fexts = [fe]

        for e in fexts:

            expected = op.join(outdir, f + e)

            allFiles.append(expected)

            print('  ', expected)

            assert op.exists(expected)

    allThatExist = os.listdir(outdir)
    allThatExist = [f for f in allThatExist if op.isfile(op.join(outdir, f))]

    assert len(allThatExist) == len(allFiles)

    for i, f in enumerate(files):
        f = fslimage.addExt(op.join(outdir, f), mustExist=True)

        if isinstance(datahashes, list):
            if len(datahashes) > len(files):
                diff = len(datahashes) - len(files)
                h    = datahashes[i + diff]

            else:
                h = datahashes[i]
        else:
            h = datahashes[op.basename(f)]

        checkImageHash(f, h)


def test_imcp_shouldPass(move=False):


    #
    # if not useDefaultExt:
    #
    #      imcp src.img dest     -> dest.img
    #      imcp src.img dest.nii -> dest.nii
    #
    # if defaultExt:
    #      imgp src.img dest     -> dest.nii.gz
    #      imgp src.img dest.nii -> dest.nii.gz

    #
    # (files_to_create,
    #    [( imcp_args, files_which_should_exist),
    #     ...
    #    ]
    # )
    shouldPass = [
        ('file.img', [
            ('file     file',     'file.img'),
            ('file     file.img', 'file.img'),
            ('file     file.hdr', 'file.img'),
            ('file     .',        'file.img'),
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
        ]),

        ('file.img file.blob', [
            ('file     file',     'file.img'),
            ('file     file.img', 'file.img'),
            ('file     file.hdr', 'file.img'),
            ('file     .',        'file.img'),
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
        ]),


        ('file.img file.nii', [
            ('file.img file',     'file.img'),
            ('file.img file.img', 'file.img'),
            ('file.img file.hdr', 'file.img'),
            ('file.img .',        'file.img'),
            ('file.hdr file',     'file.img'),
            ('file.hdr file.img', 'file.img'),
            ('file.hdr file.hdr', 'file.img'),
            ('file.hdr .',        'file.img'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),

            # TODO both img/nii files
        ]),


        ('file.nii', [
            ('file     file',     'file.nii'),
            ('file     file.nii', 'file.nii'),
            ('file     .',        'file.nii'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),
            ('file.nii .',        'file.nii'),
        ]),

        ('file.nii.gz', [
            ('file        file',        'file.nii.gz'),
            ('file        file.nii.gz', 'file.nii.gz'),
            ('file        .',           'file.nii.gz'),
            ('file.nii.gz file',        'file.nii.gz'),
            ('file.nii.gz file.nii.gz', 'file.nii.gz'),
            ('file.nii.gz .',           'file.nii.gz'),
        ]),


        ('file.nii file.blob', [
            ('file     file',     'file.nii'),
            ('file     file.nii', 'file.nii'),
            ('file     .',        'file.nii'),
            ('file.nii file',     'file.nii'),
            ('file.nii file.nii', 'file.nii'),
            ('file.nii .',        'file.nii'),
        ]),


        ('file.nii file.nii.gz', [
            ('file.nii    file',        'file.nii'),
            ('file.nii    file.nii',    'file.nii'),
            ('file.nii    .',           'file.nii'),
            ('file.nii.gz file',        'file.nii.gz'),
            ('file.nii.gz file.nii.gz', 'file.nii.gz'),
            ('file.nii.gz .',           'file.nii.gz'),

            # TODO both
        ]),

        ('file.img file.nii file.nii.gz', [
            ('file.img file.nii file.nii.gz .', 'file.img file.nii file.nii.gz'),
            ('file.img                      .', 'file.img'),
            ('file.img                      .', 'file.img'),
            ('file.nii                      .', 'file.nii'),
            ('file.nii file.nii.gz          .', 'file.nii file.nii.gz'),
        ]),


        ('001.img 002.img 003.img', [

            ('001     002     003     .', '001.img 002.img 003.img'),
            ('001.img 002.img 003.img .', '001.img 002.img 003.img'),
            ('001.hdr 002.hdr 003.hdr .', '001.img 002.img 003.img'),

            ('001.img 002     003     .', '001.img 002.img 003.img'),
            ('001.hdr 002     003     .', '001.img 002.img 003.img'),

            ('001.img 002.hdr 003.img .', '001.img 002.img 003.img'),
            ('001.hdr 002.img 003.hdr .', '001.img 002.img 003.img'),

            ('001     003             .', '001.img 003.img'),
            ('001.img 003.img         .', '001.img 003.img'),
            ('001.hdr 003.hdr         .', '001.img 003.img'),

            ('001.img 003             .', '001.img 003.img'),
            ('001.hdr 003             .', '001.img 003.img'),

            ('001.img 003.img         .', '001.img 003.img'),
            ('001.hdr 003.hdr         .', '001.img 003.img'),
        ]),
    ]


    indir  = tempfile.mkdtemp()
    outdir = tempfile.mkdtemp()

    try:

        for files_to_create, tests in shouldPass:

            files_to_create = files_to_create.split()

            for imcp_args, should_exist in tests:

                should_exist    = should_exist.split()
                imcp_args       = imcp_args.split()
                imcp_srcs       = imcp_args[:-1]
                imcp_dest       = imcp_args[ -1]

                hashes = {}
                for fn in files_to_create:
                    if looks_like_image(fn):
                        hashes[fn] = makeImage(op.join(indir, fn))
                    else:
                        hashes[fn] = make_dummy_file(op.join(indir, fn))

                print()
                print('files_to_create: ', files_to_create)
                print('imcp_srcs:       ', imcp_srcs)
                print('imcp_dest:       ', imcp_dest)
                print('should_exist:    ', should_exist)
                print('indir:           ', os.listdir(indir))

                for src in imcp_srcs:

                    print('  src: {}'.format(src))

                    src = op.join(indir, src)

                    if move: imcp.immv(src, op.join(outdir, imcp_dest), overwrite=True)
                    else:    imcp.imcp(src, op.join(outdir, imcp_dest), overwrite=True)


                print('indir after:     ', os.listdir(indir))
                print('outdir after:    ', os.listdir(outdir))

                # check file contents
                checkFilesToExpect(should_exist,
                                   outdir,
                                   None,
                                   hashes)

                # If move, check that
                # input files are gone
                if move:
                    for f in should_exist:
                         assert not op.exists(op.join(indir, f))

                for f in os.listdir(indir):
                    try:    os.remove(op.join(indir,  f))
                    except: pass

                for f in os.listdir(outdir):
                    os.remove(op.join(outdir, f))


    finally:
        shutil.rmtree(indir)
        shutil.rmtree(outdir)


def test_immv_shouldPass():
    test_imcp_shouldPass(move=True)

#!/usr/bin/env python # # test_immv_imcp.py - # # Author: <NAME> <<EMAIL>> # Checks that the given NIFTI image matches the given hash. # filename already has a different extension # # if not useDefaultExt: # #      imcp src.img dest     -> dest.img #      imcp src.img dest.nii -> dest.nii # # if defaultExt: #      imgp src.img dest     -> dest.nii.gz #      imgp src.img dest.nii -> dest.nii.gz # # (files_to_create, #    [( imcp_args, files_which_should_exist), #     ... #    ] # ) # TODO both img/nii files # TODO both # check file contents # If move, check that # input files are gone