mrc 0.3.1

Read and write .mrc and .dv (deltavision) image file format

mrc

Read and write .dv (deltavision) and some mrc image file format.

Note, this module is designed to read the MRC variant used by deltavision microscopes (.dv) and the IVE library from UCSF. For the MRC2014 file format frequently used for structural biology, see mrcfile

(though dv and mrc formats are very similar, priism/dv files that evolved from the IVE library at UCSF have a slightly different header format, preventing mrcfile from working).

Install

pip install mrc

usage and API

new API: Oct 2021

DVFile is a rewrite of the reader, and will be the only maintained reader going forward. It does not write files (see the legacy API for that).

from mrc import DVFile, imread
import numpy as np

my_array = imread('some_file.dv')                          # read to numpy array
my_array = imread('some_file.dv', dask=True)               # read to dask array
my_array = imread('some_file.dv', xarray=True)             # read to xarray
my_array = imread('some_file.dv', xarray=True, dask=True)  # read to dask-xarray

# or open a file with DVFile
f = DVFile('some_file.dv')

# attributes:   # example output
f.path          # 'some_file.dv'
f.shape         # (10, 2, 256, 256)
f.ndim          # 4
f.dtype         # np.dtype('uint16')
f.sizes         # {'T': 10, 'C': 2, 'Y': 256, 'X': 256}

# array output
f.asarray()                # in-memory np.ndarray
np.asarray(f)              # alternative to f.asarray()
f.to_dask()                # delayed dask.array.Array
f.to_xarray()              # in-memory xarray.DataArray, with labeled axes/coords
f.to_xarray(delayed=True)  # delayed xarray.DataArray

# metadata
f.hdr           # Header as a named tuple
f.ext_hdr       # (optional) extended header info
f.voxel_size    # VoxelSize(x=0.65, y=0.65, z=1.0)

f.close()       # don't forget to close when done!
f.closed        # boolean, whether the file is closed

# ... or you can use it as a context manager
with DVFile('some_file.dv') as dvf:
    xarr = dvf.to_xarray()

legacy API

The following older API still exists in this package under the mrc namespace.

This module was extracted from the priithon package, written by Sebastian Haase.

import mrc
import numpy as np

# Read a dv file
arr = mrc.imread('/path/to/file.dv')
# just a numpy array with the data...
isinstance(arr, np.ndarray)  # True

# additional info in stored in the arr.Mrc object.
# print it
arr.Mrc.info()
# or access particular fields:
print(arr.Mrc.header)
# dv files may have additional info in the extended header:
arr.Mrc.extended_header
# for instsance, timestamps for each channel at each timepoint:
arr.Mrc.extended_header['timeStampSeconds']

# or you can write a numpy array to DV format
arr = np.random.rand(23,3,256,256).astype('single')
mrc.imsave("/path/to/output.dv", arr,
    metadata={
        'dx': 0.08,
        'dy': 0.08,
        'dz': 0.125,
        'wave': [445, 528, 615, 0, 0]
    }
)

Priism (DV) MRC Header Format

this information is archived from the no-longer-existing page at http://www.msg.ucsf.edu/IVE/IVE4_HTML/priism_mrc_header.html

The MRC header is 1024 bytes layed out as described below. Each field is in one of these formats:

n Is a 2-byte signed integer (NPY_INT16)

i Is a 4-byte signed integer (NPY_INT32)

f Is a 4-byte floating-point value in IEEE format (NPY_FLOAT32)

cn Is a string of characters that is n bytes long.

Byte Numbers	Variable Type	Variable Name	Contents
1 - 4	i	NumCol	number of columns (fastest-varying dimension; normally mapped to x)
5 - 8	i	NumRow	number of rows (second fastest-varying dimension; normally mapped to y)
9 - 12	i		number of sections (slowest-varying dimension; normally mapped to the remaining dimensions, z, wavelength, and time)
13 - 16	i	PixelType	data type (see Pixel Data Types)
17 - 20	i	mxst	index of the first column (normally mapped to x) in the data; zero by default
21 - 24	i	myst	index of the first row (normally mapped to y) in the data; zero by default
25 - 28	i	mzst	index of the first section (normally treated as the first z) in the data; zero by default
29 - 32	i	mx	number of intervals in the fastest-varying direction (normally x)
33 - 36	i	my	number of intervals in the second fastest-varying direction (normally y)
37 - 40	i	mz	number of intervals in the slowest varying direction (normally treated as z)
41 - 44	f	dx	pixel spacing times sampling interval for fastest-varying direction (first cell dimension in Angstroms for crystallographic data)
45 - 48	f	dy	pixel spacing times sampling interval for second fastest-varying direction (second cell dimension in Angstroms for crystallographic data)
49 - 52	f	dz	pixel spacing times sampling interval slowest-varying direction (third cell dimension in Angstroms for crystallographic data)
53 - 56	f	alpha	cell angle (alpha) in degrees; defaults to 90
57 - 60	f	beta	cell angle (beta) in degrees; defaults to 90
61 - 64	f	gamma	cell angle (gamma) in degrees; defaults to 90
65 - 68	i		column axis (1 = x, 2 = y, 3 = z; defaults to 1)
69 - 72	i		row axis (1 = x, 2 = y, 3 = z; defaults to 2)
73 - 76	i		section axis (1 = x, 2 = y, 3 = z; defaults to 3)
77 - 80	f	min	minimum intensity of the 1st wavelength image
81 - 84	f	max	maximum intensity of the 1st wavelength image
85 - 88	f	mean	mean intensity of the first wavelength image
89 - 92	i	nspg	space group number (for crystallography)
93 - 96	i	next	extended header size in bytes.
97 - 98	n	dvid	ID value (-16224)
99 - 100	n	nblank	unused
101 - 104	i	ntst	starting time index
105 - 128	c24	blank	24 bytes long blank section
129 - 130	n	NumIntegers	number of 4 byte integers stored in the extended header per section.
131 - 132	n	NumFloats	number of 4 byte floating-point numbers stored in the extended header per section.
133 - 134	n	sub	number of sub-resolution data sets stored within the image typically 1)
135 - 136	n	zfac	reduction quotient for the z axis of the sub-resolution images
137 - 140	f	min2	minimum intensity of the 2nd wavelength image
141 - 144	f	max2	maximum intensity of the 2nd wavelength image
145 - 148	f	min3	minimum intensity of the 3rd wavelength image
149 - 152	f	max3	maximum intensity of the 3rd wavelength image
153 - 156	f	min4	minimum intensity of the 4th wavelength image
157 - 160	f	max4	maximum intensity of the 4th wavelength image
161 - 162	n	image type	see Image Types
163 - 164	n	LensNum	lens identification number
165 - 166	n	n1	depends on the image type
167 - 168	n	n2	depends on the image type
169 - 170	n	v1	depends on the image type
171 - 172	n	v2	depends on the image type
173 - 176	f	min5	minimum intensity of the 5th wavelength image
177 - 180	f	max5	maximum intensity of the 5th wavelength image
181 - 182	n	NumTimes	number of time points
183 - 184	n	ImgSequence	image sequence (0 = ZTW, 1 = WZT, 2 = ZWT)
185 - 188	f		x axis tilt angle (degrees)
189 - 192	f		y axis tilt angle (degrees)
193 - 196	f		z axis tilt angle (degrees)
197 - 198	n	NumWaves	number of wavelengths
199 - 200	n	wave1	wavelength 1 in nm
201 - 202	n	wave2	wavelength 2 in nm
203 - 204	n	wave3	wavelength 3 in nm
205 - 206	n	wave4	wavelength 4 in nm
207 - 208	n	wave5	wavelength 5 in nm
209 - 212	f	z0	z origin (um for optical, Angstroms for EM)
213 - 216	f	x0	x origin (um for optical, Angstroms for EM)
217 - 220	f	y0	y origin (um for optical, Angstroms for EM)
221 - 224	i	NumTitles	number of titles (valid numbers are between 0 and 10)
225 - 304	c80		title 1
305 - 384	c80		title 2
385 - 464	c80		title 3
465 - 544	c80		title 4
545 - 624	c80		title 5
625 - 704	c80		title 6
705 - 784	c80		title 7
785 - 864	c80		title 8
865 - 944	c80		title 9
945 - 1024	c80		title 10

Pixel Data Types

The data type used for image pixel values, stored as a signed 32-bit integer in bytes 13 through 16, is designated by one of the code numbers in the following table.

Data Type	Numpy Type	Description
0	NPY_UINT8	1-byte unsigned integer
1	NPY_INT16	2-byte signed integer
2	NPY_FLOAT32	4-byte floating-point (IEEE)
3		4-byte complex value as 2 2-byte signed integers
4	NPY_COMPLEX64	8-byte complex value as 2 4-byte floating-point (IEEE) values
5		2-byte signed integer (unclear)
6	NPY_UINT16	2-byte unsigned integer
7	NPY_INT32	4-byte signed integer

Type codes 5, 6, and 7 are not standard MRC types and are not likely to be correctly interpreted by other software that uses MRC files.

Image Types

The type of a Priism image is given by the signed 16-bit integer in header bytes 161 and 162. The meaning of these types is given in the table below. The floating-point attributes, v1 and v2, used by some image types are stored as 16-bit signed integers in the header; to do so the values are multiplied by 100 and rounded to the nearest integer when stored and are divided by 100 when retrieved.

0 (IM_NORMAL_IMAGES)

Used for normal image data.

1 (IM_TILT_SERIES)

Used for single axis tilt series with a uniform angle increment. n1 specifies the tilt axis (1 for x, 2 for y, 3 for z) and v1 the angle increment in degrees. n2 relates the coordinates in the tilt series to coordinates in a 3D volume: the assumed center of rotation is the z origin from the header plus n2 times one half of the z pixel spacing from the header. v2 is always zero.

2 (IM_STEREO_TILT_SERIES)

Used for stereo tilt series. n1 specifies the tilt axis (1 for x, 2 for y, 3 for z), v1 the angle increment in degrees, and v2 is the angular separation in degrees for the stereo pairs. n2 is always zero.

3 (IM_AVERAGED_IMAGES)

Used for averaged images. n1 is the number of averaged sections and n2 is the number of sections between averaged sections. v1 and v2 are always zero.

4 (IM_AVERAGED_STEREO_PAIRS)

Used for averaged stereo pairs. n1 is the number of averaged sections, n2 is the number of sections between averaged sections, and v2 is the angular separation in degrees for the stereo pairs. v2 is always zero.

5 (IM_EM_TILT_SERIES)

Used for EM tomography data. The tilt angles are stored in the extended header.

20 (IM_MULTIPOSITION)

Used for images of well plates. The following quantities are bit-encoded in n1 (valid range for each is show in parentheses): iwell (0-3), ishape (0-1), ibin (0-15), ispeed (0-2), igain (0-3), and mag (0-1). n2 is the number of fields per well. v1 is the fill factor (.01 to 1.5 in .01 steps). v2 is not used.

8000 (IM_PUPIL_FUNCTION)

Used for images of pupil functions. n1 and n2 are not used. v1 is the numerical aperture times ten. v2 is the immersion media refractive index times one hundred. The pixel spacings and origin have units of cycles per micron rather than microns.

Credits

This package was created by Sebastian Haase as a part of the priithon package. It is updated and maintained by Talley Lambert.