def test_scaleStack(self):
particles = self.dataset.getFile("particles/BPV_1386.stk")
outFn = join('/tmp', 'scaled.mrc')
ih = emlib.image.ImageHandler()
DT = emlib.DT_FLOAT
# Scaled with a higher dimension using finalDimension parameter
EXPECTED_SIZE = (256, 256, 131, 1)
ih.scale2DStack(particles, outFn, finalDimension=EXPECTED_SIZE[0])
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), EXPECTED_SIZE)
self.assertEqual(ih.getDataType(outFn), DT)
# Scaled with a lower dimension using finalDimension parameter
EXPECTED_SIZE = (64, 64, 131, 1)
ih.scale2DStack(particles, outFn, finalDimension=EXPECTED_SIZE[0])
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), EXPECTED_SIZE)
self.assertEqual(ih.getDataType(outFn), DT)
# Scaled with a higher dimension using scaleFactor parameter
scaleFactor = 1.5
EXPECTED_SIZE = (210, 210, 131, 1)
ih.scale2DStack(particles, outFn, scaleFactor=scaleFactor)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), EXPECTED_SIZE)
self.assertEqual(ih.getDataType(outFn), DT)
def test_convertMovie(self):
"""Check movie conversion"""
movFn = self.dsFormat.getFile('qbeta/qbeta.mrc') + ":mrcs"
ih = emlib.image.ImageHandler()
# Check that we can read the dimensions of the dm4 file:
EXPECTED_SIZE = (4096, 4096, 1, 7)
EXPECTED_DT = emlib.DT_USHORT
self.assertEqual(ih.getDimensions(movFn), EXPECTED_SIZE)
self.assertEqual(ih.getDataType(movFn), EXPECTED_DT)
outFn = join('/tmp/qbeta_converted.mrcs')
ih.convertStack(movFn, outFn, 2, 6)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), (4096, 4096, 1, 5))
self.assertEqual(ih.getDataType(outFn), EXPECTED_DT)
if pwutils.envVarOn(SCIPION_DEBUG_NOCLEAN):
print("Not cleaning output movie: ", outFn)
else:
pwutils.cleanPath(outFn)
def test_readDM4(self):
""" Check we can read dm4 files (using EMAN)
"""
micFn = self.dsFormat.getFile('SuperRef_c3-adp-se-xyz-0228_001.dm4')
ih = emlib.image.ImageHandler()
# Check that we can read the dimensions of the dm4 file:
EXPECTED_SIZE = (7676, 7420, 1, 1)
self.assertEqual(ih.getDimensions(micFn), EXPECTED_SIZE)
# We could even convert to an mrc file:
outSuffix = pwutils.replaceBaseExt(micFn, 'mrc')
outFn = join('/tmp', outSuffix)
print("Converting: \n%s -> %s" % (micFn, outFn))
ih.convert(micFn, outFn)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
# Check dimensions are still the same:
self.assertEqual(ih.getDimensions(outFn), EXPECTED_SIZE)
# Clean up tmp files
pwutils.cleanPath(outFn)
def _getMdString(self, filename, block=None):
md = emlib.MetaData()
if block:
md.read(block + '@' + filename)
else:
md.read(filename, 1)
labels = md.getActiveLabels()
msg = "Metadata items: *%d*\n" % md.getParsedLines()
msg += "Metadata labels: " + ''.join(
["\n - %s" % emlib.label2Str(l) for l in labels])
imgPath = None
for label in labels:
if emlib.labelIsImage(label):
imgPath = self._getImgPath(
filename, md.getValue(label, md.firstObject()))
if imgPath is None or not os.path.exists(imgPath):
imgPath = None
break
# If there is an image and is not too big
if imgPath and pwutils.getFileSize(imgPath) < (
pwem.Config.MAX_PREVIEW_FILE_SIZE * 1024 * 1024):
self._imgPreview = self._getImagePreview(imgPath)
self._imgInfo = self._getImageString(imgPath)
return msg
def test_createEmptyImage(self):
outFn = join('/tmp', 'empty.mrc')
SIZE = (128, 128, 1, 1)
ih = emlib.image.ImageHandler()
DT = emlib.DT_FLOAT
ih.createEmptyImage(outFn, SIZE[0], SIZE[1], dataType=DT)
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), SIZE)
self.assertEqual(ih.getDataType(outFn), DT)
def test_truncateMask(self):
ih = emlib.image.ImageHandler()
maskFn = self.dataset.getFile('masks/mask.vol')
outFn = join('/tmp', 'mask.vol')
ih.truncateMask(maskFn, outFn, newDim=128)
EXPECTED_SIZE = (128, 128, 128, 1)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), EXPECTED_SIZE)
pwutils.cleanPath(outFn)
def test_convertMicrographs(self):
""" Convert micrograhs to different formats.
EMAN2 required for .img
"""
micFn = self.dataset.getFile('micrographs/BPV_1386.mrc')
outSuffix = pwutils.replaceBaseExt(micFn, 'img')
ih = emlib.image.ImageHandler()
outFn = join('/tmp', outSuffix)
print("Converting: \n%s -> %s" % (micFn, outFn))
ih.convert(micFn, outFn)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
pwutils.cleanPath(outFn)
pwutils.cleanPath(outFn.replace('.img', '.hed'))
def _getImagePreview(self, filename):
# If file size if big
if pwutils.getFileSize(filename) > (pwem.Config.MAX_PREVIEW_FILE_SIZE *
1024 * 1024):
return
dim = 128
if isStandardImage(filename):
self.tkImg = gui.getImage(os.path.abspath(filename),
tkImage=True,
maxheight=dim)
else:
fn = self._index + filename
self.tkImg = getTkImage(self._image, fn, dim)
return self.tkImg
def test_readCompressedTIF(self):
""" Check we can read tif files
"""
micFn = self.dsFormat.getFile('c3-adp-se-xyz-0228_200.tif')
ih = emlib.image.ImageHandler()
# Check that we can read the dimensions of the dm4 file:
EXPECTED_SIZE = (7676, 7420, 1, 38)
self.assertEqual(ih.getDimensions(micFn), EXPECTED_SIZE)
# We could even convert to an mrc file:
outSuffix = pwutils.replaceBaseExt(micFn, 'mrc')
outFn = join('/tmp', outSuffix)
print("Converting: \n%s -> %s" % ((1, micFn), outFn))
ih.convert((1, micFn), outFn)
self.assertTrue(os.path.exists(outFn))
self.assertTrue(pwutils.getFileSize(outFn) > 0)
self.assertEqual(ih.getDimensions(outFn), (7676, 7420, 1, 1))
# Clean up tmp files
pwutils.cleanPath(outFn)
def size(self):
s = 0
for f in self.files:
s += pwutils.getFileSize(f)
return s
