def get_raw_data(self, index):
# Use mrcfile to open the dataset and extract slice index from the stack.
# Note MRC files use z, y, x ordering
with mrcfile.mmap(self._image_file) as mrc:
raw_data = mrc.data[index, ...]
return flex.double(raw_data.astype("double")) + self.pedestal
def __init__(self, Data, filename, stats=None):
self._data_obj = Data
self.filename = filename
super(MRC, self).__init__()
self.file = mrcfile.mmap(filename, 'r')
self.dtype = self.file.data.dtype
def _start(self):
"""Open the MRC file, read the metadata into an internal dictionary
self._header_dictionary, add FEI extended metadata if available"""
with mrcfile.mmap(self._image_file) as mrc:
h = mrc.header
#xh = mrc.extended_header
self._header_dictionary = self._unpack_header(h)
if h['exttyp'].tobytes() == b'FEI1':
try:
xh = self._read_ext_header(self._image_file)
self._header_dictionary.update(xh)
except KeyError:
pass
# Add a positive pedestal level to images to avoid negative
# pixel values if a value is set by the environment variable
# ADD_PEDESTAL. This is a nasty workaround! Suitable values might be
# +128 for Ceta and +8 for Falcon III (https://doi.org/10.1101/615484)
self.pedestal = float(os.environ.get("ADD_PEDESTAL", 0))
# Set all negative pixel values to zero (after applying the pedestal).
# Another nasty hack, while we explore what is the best practice for
# images that have negative-valued pixels
self.truncate = "TRUNCATE_PIXELS" in os.environ
def scale(origin_path, new_path, scale_rate=1):
origin_mrc = mrcfile.mmap(origin_path, 'r')
origin_shape = np.array(origin_mrc.data.shape)
ox, oy, oz = origin_shape
scale = SCALE_BASE**scale_rate
new_shape = (origin_shape + scale - 1) // scale
nx, ny, nz = new_shape
new_mrc = mrcfile.new_mmap(new_path, (nz, nx, ny),
mrc_mode=mrcfile.utils.mode_from_dtype(
mrcfile.utils.data_dtype_from_header(
origin_mrc.header)),
overwrite=True)
print('scaling data')
for z in tqdm(range(nz)):
sz = z * scale
for x in range(nx):
sx = x * scale
for y in range(ny):
sy = y * scale
new_mrc.data[z, x, y] = np.mean(
origin_mrc.data[sz:min(sz + scale, oz),
sx:min(sx + scale, ox),
sy:min(sy + scale, oy)])
print('updating header')
new_mrc.update_header_stats()
print('header updated')
origin_mrc.close()
new_mrc.close()
def get_raw_data(self, index):
# Note MRC files use z, y, x ordering
with mrcfile.mmap(self._image_file) as mrc:
image = flex.double(mrc.data[index, ...].astype("double"))
return image
def _init_data(self, nx, ny=None, nz=None):
''' Init data with zeros. All arguments are truncated to int silently.
Args:
nx: A `int`. The x dimension of the image
ny: A `int`. The y dimension of the image. default is 1
nz: A `int`. The z dimension of the image. Default is 1
'''
nx = int(nx)
if nx <= 0:
raise ValueError("Wrong value for x dimension")
dims = [nx]
if ny is not None:
ny = int(ny)
if ny <= 0:
raise ValueError("Wrong value for y dimension")
dims = [ny] + dims
if nz is not None:
nz = int(nz)
if nz <= 0:
raise ValueError("Wrong value for z dimension")
dims = [nz] + dims
if not self._mmap:
self.data = np.zeros(dims, self.dtype)
else:
mrc = mrcfile.mmap(self._mmap_file, mode=self._mmap_mode)
mrc._open_memmap(np.float32, tuple(dims))
mrc.update_header_from_data()
self.data = mrc.data
def from_mrcfile(Class, filename):
"""
Read the simulated data from a mrc file
Args:
filename (str): The input filename
"""
# Read the data
handle = mrcfile.mmap(filename, "r")
# Check the header info
if handle.header.exttyp == b"FEI1":
assert handle.extended_header.dtype == FEI_EXTENDED_HEADER_DTYPE
assert len(handle.extended_header.shape) == 1
assert handle.extended_header.shape[0] == handle.data.shape[0]
# Read the angles
angle = np.zeros(handle.data.shape[0], dtype=np.float32)
for i in range(handle.extended_header.shape[0]):
angle[i] = handle.extended_header[i]["Alpha tilt"]
position = np.zeros(shape=(handle.data.shape[0], 3),
dtype=np.float32)
drift = np.zeros(shape=(handle.data.shape[0], 2), dtype=np.float32)
defocus = np.zeros(shape=(handle.data.shape[0]), dtype=np.float32)
for i in range(handle.extended_header.shape[0]):
# Read the positions
position[i, 0] = handle.extended_header[i]["Shift X"]
position[i, 1] = handle.extended_header[i]["Shift Y"]
position[i, 2] = handle.extended_header[i]["Z-Stage"]
# Read the drift
drift[i, 0] = handle.extended_header[i]["Shift offset X"]
drift[i, 1] = handle.extended_header[i]["Shift offset Y"]
# Read the defocus
defocus[i] = handle.extended_header[i]["Defocus"]
else:
angle = np.zeros(handle.data.shape[0], dtype=np.float32)
position = np.zeros(shape=(handle.data.shape[0], 3),
dtype=np.float32)
drift = np.zeros(shape=(handle.data.shape[0], 2), dtype=np.float32)
defocus = np.zeros(handle.data.shape[0], dtype=np.float32)
# Get the pixel size
pixel_size = handle.voxel_size["x"]
# Create the reader
return Reader(
handle,
handle.data,
angle,
position,
pixel_size,
drift=drift,
defocus=defocus,
)
def volread(self, path):
"""Helper to return a file handle to an HDF5 file.
Args:
path (str): Path to the HDF5 file.
Raises:
Exception: If the file is not and HDF5 file.
Returns:
h5py.File: File handle to an HDF5 file.
"""
_, file_extension = os.path.splitext(path)
data = None
logger.info("Loading file handle")
if file_extension in [".hdf5", ".h5"]:
data = h5.File(path, "r")
elif file_extension in [".tif", ".tiff"]:
data = io.imread(path)
elif file_extension in [".rec", ".mrc"]:
mrc = mrcfile.mmap(path, mode="r+")
data = mrc.data
else:
raise Exception("File format not supported")
return data
def __init__(self, path, scale_rate=0):
self.base_path = path
self.scale_rate = scale_rate
self.path = self.get_path(self.base_path, self.scale_rate)
self.next = None
self.mrc = mrcfile.mmap(self.path, 'r')
self._check_scale()
def write(cls, filename, data, filepath=None, mrcfh=None, exheader=None):
'''
Return writed mrc filehandle
-------------------------------
This class method write will write an
mrcfile by copy parameters
from existing mrc or mannually input
'''
print(mrcfh)
if filepath == None:
filepath = os.getcwd()
if not (mrcfh or exheader):
raise ValueError('Not enough parameters to \
write mrcfile')
if exheader:
pass
else:
_mrc = mrcfile.mmap(mrcfh)
# header = _mrc.header
exheader = _mrc.extended_header
# volsize = _mrc.voxel_size
_mrc.close()
filehandle = os.path.join(filepath, filename)
with mrcfile.new(filehandle) as mrc:
mrc.set_data(data)
# print(mrc._check_writeable())
# mrc._set_voxel_size(volsize)
mrc.set_extended_header(exheader)
return filehandle
def loader(imageblock):
if mmap is True:
mrc = mrcfile.mmap(image_path)
else:
mrc = mrcfile.open(image_path)
imageblock.data = mrc.data
pixel_size = structured_to_unstructured(mrc.voxel_size)[::-1]
imageblock.pixel_size = pixel_size
def mrc_from_uri(uri, mode="a", shape=None, dtype="float32", fill=0):
"""
Loads a MRC dataset from an uri of the form:
`[mrc://]file`
Where `file` is the path to the `.mrc` or `.rec` file.
Parameters
----------
uri: string
A file URI for a dataset in MRC format.
mode: one of ['a', 'r', 'r+', 'w']
The opening mode. See `open` for more details.
shape: tuple
Shape of the ND-Array. Only valid if `mode='a'`.
dtype: numpy-accepted data type
Data type of the ND-Array. Only valid if `mode='a'`. Default: float32.
fill: int or float
Value used to fill the array. Default: 0.
"""
match = re.match(MRC_REGEXP, uri)
if match is None:
raise ValueError("Invalid mrc:// uri: `{}`".format(uri))
fpath = match.group("fpath")
if mode != "r":
if mode in ["a", "r+"] and op.isfile(fpath):
f = mrc.mmap(fpath, "r+")
if not sameshape(f.data.shape, shape) or not samedtype(f.data.dtype, dtype):
msg = (
"Dataset already exists with different"
" shape or dype. Expected {} and {}, got {} and {}".format(
shape, dtype, f.data.shape, f.data.dtype
)
)
raise ValueError(msg)
else:
f = mrc.MrcMemmap(fpath, mode="w+", overwrite=True)
f._open_memmap(dtype, shape)
f.update_header_from_data()
f.data[...] = fill
else:
f = mrc.mmap(fpath, "r")
return DatasetWrapper(f, f.data)
def __init__(self, path, mode='r'):
self.path = path
self.mode = mode
if mrcfile is None:
raise AttributeError("mrcfile is not available")
try:
self._f = mrcfile.mmap(self.path, self.mode)
except ValueError:
self._f = mrcfile.open(self.path, self.mode)
def Input_read(dir, suffix):
files = glob(dir + '/*.' + suffix)
L = len(files)
if L == 0:
print('no file exists')
return -1, -1, -1, -1, -1
else:
print(str(len(files)) + ' files in ', dir)
(x, y, z) = mrcfile.mmap(files[0]).data.shape
raw_input = np.zeros(dtype=np.uint8, shape=[L, x, y, z, 1])
for filei in range(L):
mrc = mrcfile.mmap(files[filei])
content = np.array(mrc.data)
mrc = 0
rshape = np.array(content).reshape([1, x, y, z, 1])
# print(rshape)
raw_input[filei, :] = rshape[:]
return raw_input, L, files
def showCtfMicrographs(self, projectDirectory, ctfs):
allMicrographs = []
for i in range(len(ctfs)):
fileName = ctfs[i]['ctfImage'].replace(':mrc', '')
try:
mrc = mrcfile.mmap(projectDirectory + fileName)
except (FileNotFoundError, ValueError) as err:
self.errorText.value = "Unable to load Micrograph: {0}".format(
err)
self.errorText.layout = self.errorLayout
else:
#extract data, convert values to 0 - 255 int8 format
formatted = (mrc.data[0] * 255 /
np.max(mrc.data)).astype('uint8')
img = Image.fromarray(formatted)
img.thumbnail(self.thumbNailSize)
imagePng = self.convertToPNG(img)
mrc.close()
#Dynamically build the Ctf mrcs and buttons.
img = widgets.Image(value=imagePng,
format='PNG',
width=self.thumbNailSize[0],
height=self.thumbNailSize[1])
dataButton = widgets.Button(description='Data',
disabled=False,
button_style='',
tooltip='Show data',
icon='check')
mrcButton = widgets.Button(description='Raw mrc',
disabled=False,
button_style='',
tooltip='Show micrograph',
icon='check')
buttonOutput = widgets.Output(layout={'border': '2px solid black'})
dataButton.add_traits(showData=traitlets.Any(buttonOutput))
mrcButton.add_traits(showMrc=traitlets.Any(buttonOutput))
#adding on_click actions to buttons dynamically, lambda is an anonymous function
#lambda arguments: function
dataButton.on_click(lambda dataButton, num=i: self.dynamicOnClick(
ctfs[num], dataButton))
mrcButton.on_click(lambda mrcButton, num=i: self.dynamicOnClick(
ctfs[num], mrcButton))
micrograph = VBox(
[img, HBox([dataButton, mrcButton]), buttonOutput])
allMicrographs.append(micrograph)
return allMicrographs
def crop_mrc(mrc_path,
crop_path,
x=0,
y=0,
z=0,
dx=100,
dy=100,
dz=100,
print_header_diff=False):
"""Crop specified part of a 3d mrc file, position cropped: mrc.data[x:x+dx, y:y+dy, z:z+dz].
Note that the axis order of mrc data is (x, y, z), different from that downstream tasks use, eg. read_mrc_data and imod: (z, y, x).
Arguments:
mrc_path -- source mrc file path
crop_path -- destination path of cropped mrc file
Keyword Arguments:
x {int} -- lowerbound x coordinate to crop (default: {0})
y {int} -- lowerbound y coordinate to crop (default: {0})
z {int} -- lowerbound z coordinate to crop (default: {0})
dx {int} -- length of x to crop (default: {100})
dy {int} -- length of y to crop (default: {100})
dz {int} -- length of z to crop (default: {100})
print_header_diff {bool} -- whether to print difference between the cropped and original (default: {False})
"""
# Use mmap for faster reading large mrcfile
with mrcfile.mmap(mrc_path,
mode='r') as mrc, mrcfile.new(crop_path) as mrc_crop:
mrc_crop.set_data(
mrc.data[x:x + dx, y:y + dy, z:z +
dz]) # set_data automatically syncs header info with data
mrc_crop.voxel_size = mrc.voxel_size
mrcfile.validate(crop_path)
# Print header diff
if print_header_diff:
mrc_header = io_file.read_mrc_header(mrc_path)
crop_header = io_file.read_mrc_header(crop_path)
diffs = []
for (k1, v1), (k2, v2) in zip(mrc_header.items(), crop_header.items()):
if k1 == k2 and v1 != v2:
if isinstance(v1, dict):
assert len(v1) == len(
v2), "Different dict size: {}, {}".format(
len(v1), len(v2))
diff_dict = {
k: (v1[k], v2[k])
for k in v1 if k in v2 and v1[k] != v2[k]
}
print("diff key: ", k1, "\ndiff_dict:\n", diff_dict)
else:
print("diff key: ", k1, "\n", v1, "\n", v2, "\n")
diffs.append((v1, v2))
print("# diffs: ", len(diffs))
def run(body): # body is reference to the main Import class
files_map = []
for f in body.files_all:
fl = f.lower();
if fl.endswith(('.map', '.mrc')):
files_map.append ( f )
if len(files_map) <= 0:
return
body.file_stdout.write ( "\n" + "%"*80 + "\n" )
body.file_stdout.write ( "%%%%% Map volume data\n" )
body.file_stdout.write ( "%"*80 + "\n" )
mapSecId = "map_sec_" + str(body.widget_no)
body.widget_no += 1
pyrvapi.rvapi_add_section ( mapSecId, "Map", body.report_page_id(),
body.rvrow, 0, 1, 1, False )
k = 0
for f in files_map:
body.files_all.remove ( f )
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), f, body.summary_row, 0 )
fpath = os.path.join ( body.importDir(), f );
with mrcfile.mmap(fpath) as mrc:
msg = "MAP {0} x {1} x {2}".format(mrc.header.nx, mrc.header.ny, mrc.header.nz)
pyrvapi.rvapi_put_table_string ( body.import_summary_id(), msg, body.summary_row, 1 )
map_ = dtype_map.DType ( body.job_id )
map_.subtype = ['final_map']
map_.setFile ( f )
body.dataSerialNo += 1
map_.makeDName ( body.dataSerialNo )
body.outputDataBox.add_data ( map_ )
# Essential to rename uploaded file to put it in output directory
# Might be better to use the standard register() method instead if possible?
# Currently the file ends up remaining in the upload directory on the front end,
# even though it's removed on the number cruncher...
os.rename ( fpath, os.path.join(body.outputDir(), f) )
body.file_stdout.write ( "... processed: " + f + "\n" )
k += 1
body.rvrow += 1
pyrvapi.rvapi_flush()
return
def get_raw_data(self):
# Use mrcfile to open the dataset and the image.
# Note MRC files use z, y, x ordering
with mrcfile.mmap(self._image_file) as mrc:
image = flex.double(mrc.data.astype("double"))
image += self.pedestal
if self.truncate:
image.set_selected((image < 0), 0)
return image
def dynamicOnClick(self, ctfData, button):
if hasattr(button, 'showData'):
button.showData.clear_output()
with button.showData:
print('Defocus U: ' + str(ctfData['defocusU']) + '\n' + \
'Defocus V: ' + str(ctfData['defocusV']) + '\n' + \
'Defocus Angle: ' + str(ctfData['defocusAngle']) + '\n' + \
'Voltage: ' + str(ctfData['voltage']) + '\n' + \
'Spherical Aberration: ' + str(ctfData['sphericalAberration']) + '\n' + \
'Amplitude Contrast: ' + str(ctfData['ampContrast']) + '\n' + \
'Magnification: ' + str(ctfData['magnification']) + '\n' + \
'Detector Pixel Size: ' + str(ctfData['detectorPixelSize']) + '\n' + \
'Figure of Merit: ' + str(ctfData['figOfMerit']) + '\n' + \
'Ctf Max Resolution: ' + str(ctfData['maxResolution']))
if hasattr(button, 'showMrc'):
button.showMrc.clear_output()
with button.showMrc:
fileName = ctfData['micrographNameNoDW']
#Problem, MotionCorr2 created mrcs have an issue with the MAP ID string in the header, it should be 'MAP ' but MotionCorr ones have 'MAP'.
#Opening in permissive mode and catching the warning, we can get around this.
try:
with warnings.catch_warnings(record=True) as w:
mrc = mrcfile.mmap(self.projectDirectory.value +
fileName,
permissive=True)
except FileNotFoundError as err:
self.errorText.value = "Unable to load Micrograph: {0}".format(
err)
self.errorText.layout = self.errorLayout
else:
mrcArray = np.array(mrc.data)
#extract data, convert values to 0 - 255 int8 format
formatted = (mrcArray * 255 /
np.max(mrcArray)).astype('uint8')
img = Image.fromarray(formatted)
img.thumbnail(self.rawThumbNailSize)
#increase contast to aid visibility
enhancer = ImageEnhance.Contrast(img)
img = enhancer.enhance(6)
imagePng = self.convertToPNG(img)
mrc.close()
img = widgets.Image(value=imagePng,
format='PNG',
width=self.rawThumbNailSize[0],
height=self.rawThumbNailSize[1])
display(img)
def read(filename, mode="r"):
"""
Read the input map file
Args:
filename (str): The map filename
Return
object: The map file
"""
logger.info("Reading %s" % filename)
return mrcfile.mmap(filename, mode=mode)
def __init__(self, filehandle, validate=False):
'''
This initialize function only open .mrc file with
mmap read-only
'''
super(Mrc, self).__init__()
self.filehandle = filehandle
self.mrc = mrcfile.mmap(filehandle, mode='r')
if validate:
print('*' * 20 + 'Validating start' + '*' * 20)
if not mrcfile.validate(filehandle):
raise ValueError('Initial Mrc File is not validated')
print('*' * 20 + 'Validating finished' + '*' * 20)
'''
def reader_function(path):
"""Take a path or list of paths and return a list of LayerData tuples.
Readers are expected to return data as a list of tuples, where each tuple
is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
both optional.
Parameters
----------
path : str or list of str
Path to file, or list of paths.
Returns
-------
layer_data : list of tuples
A list of LayerData tuples where each tuple in the list contains
(data, metadata, layer_type), where data is a numpy array, metadata is
a dict of keyword arguments for the corresponding viewer.add_* method
in napari, and layer_type is a lower-case string naming the type of layer.
Both "meta", and "layer_type" are optional. napari will default to
layer_type=="image" if not provided
"""
# handle both a string and a list of strings
paths = [path] if isinstance(path, str) else path
# optional kwargs for the corresponding viewer.add_* method
# https://napari.org/docs/api/napari.components.html#module-napari.components.add_layers_mixin
add_kwargs = {}
# optional, default is "image"
layer_type = "image"
# load all files into array
layer_data = []
for _path in paths:
# Read mrcfile as a memory mapped file
data = mrcfile.mmap(_path, permissive=True).data
# Append two layers if the data type is complex
if data.dtype in [np.complex64, np.complex128]:
layer_data.append((np.abs(data), {
"name": "amplitude"
}, layer_type))
layer_data.append((np.angle(data), {"name": "phase"}, layer_type))
else:
layer_data.append((data, add_kwargs, layer_type))
return layer_data
def load_image(self, drc: str=None) -> "np.array":
"""Loads the image corresponding to this item"""
import mrcfile
if not drc:
drc = "."
drc = Path(drc)
map_file = Path(self.MapFile)
if not map_file.exists():
map_file = drc / Path(self.MapFile).name
m = mrcfile.mmap(map_file)
s = self.MapSection
return np.array(m.data[s])
def read_ptcl_mrc(ptcl_star,
transform=False,
fft_mask=None,
clipbox=None,
background_mask=None,
recenter=False):
'''
Particle mrc data
'''
# Read particle data
particle_image_num, particle_image_name = ptcl_star['rlnImageName'].split(
'@')
with mrcfile.mmap(particle_image_name, mode='r') as mrc_data:
if len(mrc_data.data.shape) == 3:
img2D = mrc_data.data[int(particle_image_num) - 1]
else:
img2D = mrc_data.data
# If transform is ON, transform the ptcl image and rest the offset distance and angles
if transform:
img2D = transform_ptcl_img2D(img2D, ptcl_star)
# Check pass filter options
if fft_mask is not None:
img2D = fft_filter(img2D, fft_mask)
# Get img center
img_origin = [0, 0]
# If recenter option is on
if recenter:
fracX, intX = math.modf(ptcl_star['rlnOriginX'])
fracY, intY = math.modf(ptcl_star['rlnOriginY'])
img_origin = [intX, intY]
# Check for clip
img2D = clip_img2D(img2D, clipbox, origin=img_origin)
# Normalize using the background mask
if background_mask is not None:
img2D = norm_intensity(img2D,
background_mask,
new_mean=0.0,
new_std=1.0)
return np.copy(img2D)
def __getitem__(self, idx):
if self.data_type == 'even':
idx = 2 * idx
elif self.data_type == 'odd':
idx = 2 * idx + 1
with torch.no_grad():
if self.dataset == 'Betagal':
with mrcfile.open(self.ParticlePath + str(idx).zfill(6) +
".mrc") as m:
image = np.array(m.data, dtype=np.float32)
if self.args.GaussianFilterProjection:
image = scipy.ndimage.gaussian_filter(
image,
self.args.GaussianSigma,
)
image = Tensor(image).unsqueeze(0).cuda()
elif self.dataset in ['Betagal-Synthetic']:
with mrcfile.mmap(self.ImageStack[idx],
permissive=True,
mode='r+') as m:
image = m.data
if self.args.GaussianFilterProjection:
image = scipy.ndimage.gaussian_filter(
image, self.args.GaussianSigma)
image = Tensor(image).unsqueeze(0).cuda()
else:
image = self.ImageStack[idx]
image = Tensor(image).unsqueeze(0).cuda()
downsampling = image.shape[-1] // self.args.RawProjectionSize
if downsampling > 1:
image = torch.nn.functional.avg_pool2d(image,
kernel_size=downsampling,
stride=downsampling,
padding=0)
if self.args.NormalizeProjections:
image = (image - image.mean()) / image.std()
return image
def read_mrc(image_path, name_regex=None, lazy=True, **kwargs):
"""
read an mrc file and return an ImageBlock
"""
name = guess_name(image_path, name_regex)
with mrcfile.mmap(image_path) as mrc:
if lazy:
data = da.from_array(mrc.data)
else:
data = np.asarray(mrc.data)
pixel_size = structured_to_unstructured(mrc.voxel_size)[::-1]
ib = ImageBlock(data=data, pixel_size=pixel_size, name=name)
logger.debug(f'succesfully read "{image_path}", {lazy=}')
return ib
def load_image(self, drc: str = None) -> 'np.array':
"""Loads the image corresponding to this item."""
import mrcfile
if not drc:
drc = self.data_drc
drc = Path(drc)
map_file = Path(self.MapFile)
if not map_file.exists():
map_file = drc / Path(self.MapFile).name
m = mrcfile.mmap(map_file)
s = self.MapSection
if m.is_single_image() and s == 0:
return np.array(m.data)
else:
return np.array(m.data[s])
def read_mrc(self, filename):
''' Read mrc file through
'''
# permissive is to go throught invalid mrc file like generated by
# motioncor2.... MotionCor2 does not write "MAP" into header...
with warnings.catch_warnings():
warnings.simplefilter("ignore")
mrc = mrcfile.mmap(filename, self._mmap_mode, permissive=True)
if self._mmap:
# logger.debug("Using mmaped file: %s" % filename)
self._mmap_file = filename
self.data = np.memmap(self._mmap_file,
dtype=mrc.data.dtype,
mode=self._mmap_mode,
offset=mrc.data.offset,
shape=mrc.data.shape)
else:
self.data = mrc.data.copy()
return self
def mrc_central_slice(filename):
# MrcMemmap reads dtype and shape from header
# https://github.com/ccpem/mrcfile/blob/master/mrcfile/mrcmemmap.py#L92
f = mrcfile.mmap(filename, permissive=True)
# mrcfile can be 2D, should check for that
ndim = len(f.data.shape)
if ndim == 2:
data = f.data
elif ndim == 3:
central_slice = f.data.shape[0] // 2
data = f.data[central_slice]
else:
f.close()
sys.exit(-1)
f.close()
return data
def __init__(self, path_to_mrc, tile_size, tile_stride,
shuffled=False, verbose=False):
self.path_to_mrc = path_to_mrc
self.mmap = mrcfile.mmap(path_to_mrc)
if verbose:
print(path_to_mrc)
self._depleted = False
length, width, height = self.mmap.data.shape
self.cols = (width // tile_stride)
self.rows = (height // tile_stride)
self.tile_size = tile_size
self.tile_stride = tile_stride
self._i = 0
self.shuffled = shuffled
if self.shuffled:
self.I = list(range(len(self)))
shuffle(self.I)
self.verbose = verbose
