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||Type || Extension || Read || Write || 3D || stack || Comments ||
||MRC || mrc || Y || Y || Y || N || ||
||Spider || spi || Y || Y || || Y || ||
||Imagic || img/hed || Y || Y || || Y || ||
||HDF || hdf || Y || Y || Y || Y || ||
||DM3 || dm3|| || Y || || || ||
||TIFF || tiff/tif || || || || || ||
||PGM || pgm || || || || || ||
||LST || lst || Y || || || || ||
||PIF || pif || || || || || ||
||VTK || || || || || || ||
||PNG || png || || || || || ||
||SAL || || || || || || ||
||ICOS || || || || || || ||
||EMIM || || || || || || ||
||Gatan2 || || || || || || ||
||Amira || || || || || || ||
||XPLOR || || || || || || ||
||EM || em || || || || || ||
||V4L || || || || || || ||
||JPEG || jpg/jpeg || || || || || ||
||FITS || || || || || || ||
||LSTFAST || || || || || || ||		 <<TableOfContents>>

= Table of supported image formats in EMAN2 =
||Type ||Extension ||Read ||Write ||3D ||Image Stacks ||Region I/O ||Comments ||
||BDB ||N/A ||Y ||Y ||Y ||Y ||Y ||This entry is for EMAN2's embedded database system, used by default for most operations. For portability see HDF5. BDB and HDF5 are the only 2 formats that support the full EMAN2 Metadata. These files are in EMAN2DB directories and should not be manipulated manually. Please see [[http://blake.bcm.edu/emanwiki/EMAN2/DatabaseWarning|this important note]] ||
||HDF5 ||hdf ||Y ||Y ||Y ||Y ||Y ||HDF5 is an international standard for scientific data (http://www.hdfgroup.org/HDF5/). It supports arbitrary metadata (header info) and is very portable. This is the standard interchange format for EMAN2. Chimera can read EMAN2 style HDF files. ||
|| || || || || || || || ||
||DM2 (Gatan)||dm2 ||Y ||N ||N ||N ||N ||Proprietary Gatan format (older version) ||
||DM3 (Gatan) ||dm3 ||Y ||N ||N ||N ||N ||Proprietary Gatan format from Digital Micrograph ||
||EM ||em ||Y ||Y ||Y ||N ||Y ||As produced by the EM software package ||
||ICOS ||icos ||Y ||Y ||Y ||N ||Y ||Old icosahedral format ||
||Imagic ||img/hed ||Y ||Y ||Y ||Y ||Y ||This format stores header and image data in 2 separate files. Region I/O is only available for 2D. The Imagic ||MRC ||mrc ||Y ||Y ||Y ||N ||Y ||Largely compatible with CCP4. Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This ||Spider ||spi ||Y ||Y ||Y ||Y ||Y ||To read the overall image header in a stacked spider file, use image_index = -1. ||
|| || || || || || || || ||
||Amira ||am ||Y ||Y ||Y ||N ||N ||A native format for the Amira visualization package ||
||DF3 ||df3 ||Y ||Y ||Y ||N ||N ||File format for POV-Ray, support 8,16,32 bit integer per pixel ||
||FITS ||fts ||Y ||N ||Y ||N ||N ||Widely used file format in astronomy ||
format in EMAN2 is fully compatible with Imagic4D standard since the 2.0 release. ||
||JPEG ||jpg/jpeg ||N ||Y ||N ||N ||N ||Note that JPEG images use lossy compression and are NOT suitable for quantitative analysis. PNG (lossless compression) is a better alternative unless file size is of critical importance. ||
||LST ||lst ||Y ||Y ||Y ||Y ||N ||ASCII file contains a list of image file names and numbers. Used in EMAN1 to avoid large files. Not commonly used in EMAN2 ||
||LSTFAST ||lsx/lst ||Y ||Y ||Y ||Y ||N ||Optomized version of LST ||
behavior is partially supported in EMAN, but be aware that it is impossible to store metadata about each image in the stack when doing this, so it is not suitable as an export format for single particle work. EMAN2 support reading of FEI MRC, which is an extended MRC format for tomography. The extra header information will be read into the header. All FEI MRC images will be 2-byte integer. ||
||OMAP ||omap ||Y ||N ||Y ||N ||N ||Also called DSN6 map, 1 byte integer per pixel ||
||PGM ||pgm ||Y ||Y ||N ||N ||N ||Standard graphics format with 8 bit greyscale images. No compression. ||
||PIF ||pif ||Y ||Y ||Y ||Y ||N ||Purdue Image Format. Images in PIF stack are homogenous. PIF doesn't currently work. ||
||PNG ||png ||Y ||Y ||N ||N ||N ||Excellent format for presentations. Lossless data compression, 8 bit or 16 bit per pixel ||
||SAL ||hdr/img ||Y ||N ||N ||N ||N ||Scans-A-Lot. Old proprietary scanner format. Separate header and data file ||
||SITUS ||situs ||Y ||Y ||Y ||N ||N ||Situs-specific ASCII format on a cubic lattice. Used by Situs programs ||
||TIFF ||tiff/tif ||Y ||Y ||N ||N ||N ||Good format for use with programs like photoshop. Some variants are good for quantitative analysis, but JPEG compression should be avoided. ||
||V4L ||v4l ||Y ||N ||N ||N ||N ||Used by some video-capture boards in Linux. Acquires images from the V4L2 interface in real-time(video4linux). ||
||VTK ||vtk ||Y ||Y ||Y ||N ||N ||Native format from Visualization Toolkit ||
||XPLOR ||xplor ||Y ||Y ||Y ||N ||N ||8 bytes integer, 12.5E float ASCII format ||


= Saving EMData from Python =
If you want to be prompted to supply a image name using a standard dialog use this approach

{{{#!python

# save a single image
a = test_image()
from emsave import save_data
save_data(a)

# save a list of images as a stack
b = test_image(2)
save_data([a,b])
}}}
= Regional I/O =
Regional I/O means you can read/write a part of an image from/to a image file. This is useful when you process a huge image file on a computer with limited resource. The region specification is the same as in EMData::get_clip() function. For regional reading, you can specify a region inside an image, partially out of image bounds, or even completely out of image bounds. For regional writing, the region must be completely inside image bounds. You need be aware when reading a partially out of bounds region from HDF5 file, it will involve copying the inbound part image to the region size memory. That means there is a performance overhead for partially out bounds region reading.

{{{#!python

# Read a origin at (1,1,1), size 8x8x8 subregion from an 64x64x64 image file 3dimage.hdf
img = EMData
region = Region(1,1,1,8,8,8)
img.read_image("3dimage.hdf",0,False,region)
}}}
= Storage type for MRC =
Pixel size of image data inside EMAN2 is float. For MRC image, by default it's writed as float (4bytes/32bit). EMAN2 also support writing short (2bytes/16bit) MRC and byte (8bit) MRC.

{{{
img = EMData(128,128)
img.write('float-image.mrc') #by default, image will be write as float
img.write_image('short-image.mrc', 0, EMUtil.ImageType.IMAGE_MRC, False, None, EMUtil.EMDataType.EM_SHORT) #write mrc file in short (16bit)
img.write_image('byte-image.mrc', 0, EMUtil.ImageType.IMAGE_MRC, False, None, EMUtil.EMDataType.EM_UCHAR) #write mrc file in byte (8bit)
}}}
In the last write_image() funciton call, 'byte-image.mrc' is the file name you write to. Second argument, 0 is the image index in a stack. It's always 0 since MRC does not support stack. third argument, EMUtil.ImageType.IMAGE_MRC is the file type you are writing to, type 'help(EMUtil.ImageType)' in python will print out all type supported by EMAN2. forth argument, False means NOT header only. fifth argument, None means we are not doing Region I/O. sixth argument, EMUtil.EMDataType.EM_UCHAR specify the data storage type for this image file. type 'help(EMUtil.EMDataType)' will list all datatypes. For MRC, three types are supported.

Contents

  1. Table of supported image formats in EMAN2
  2. Saving EMData from Python
  3. Regional I/O
  4. Storage type for MRC

Table of supported image formats in EMAN2

Type

Extension

Read

Write

3D

Image Stacks

Region I/O

Comments

BDB

N/A

Y

Y

Y

Y

Y

This entry is for EMAN2's embedded database system, used by default for most operations. For portability see HDF5. BDB and HDF5 are the only 2 formats that support the full EMAN2 Metadata. These files are in EMAN2DB directories and should not be manipulated manually. Please see this important note

HDF5

hdf

Y

Y

Y

Y

Y

HDF5 is an international standard for scientific data (http://www.hdfgroup.org/HDF5/). It supports arbitrary metadata (header info) and is very portable. This is the standard interchange format for EMAN2. Chimera can read EMAN2 style HDF files.

DM2 (Gatan)

dm2

Y

N

N

N

N

Proprietary Gatan format (older version)

DM3 (Gatan)

dm3

Y

N

N

N

N

Proprietary Gatan format from Digital Micrograph

EM

em

Y

Y

Y

N

Y

As produced by the EM software package

ICOS

icos

Y

Y

Y

N

Y

Old icosahedral format

Imagic

img/hed

Y

Y

Y

Y

Y

This format stores header and image data in 2 separate files. Region I/O is only available for 2D. The Imagic

MRC

mrc

Y

Y

Y

N

Y

Largely compatible with CCP4. Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This

Spider

spi

Y

Y

Y

Y

Y

To read the overall image header in a stacked spider file, use image_index = -1.

Amira

am

Y

Y

Y

N

N

A native format for the Amira visualization package

DF3

df3

Y

Y

Y

N

N

File format for POV-Ray, support 8,16,32 bit integer per pixel

FITS

fts

Y

N

Y

N

N

Widely used file format in astronomy

format in EMAN2 is fully compatible with Imagic4D standard since the 2.0 release. ||

JPEG

jpg/jpeg

N

Y

N

N

N

Note that JPEG images use lossy compression and are NOT suitable for quantitative analysis. PNG (lossless compression) is a better alternative unless file size is of critical importance.

LST

lst

Y

Y

Y

Y

N

ASCII file contains a list of image file names and numbers. Used in EMAN1 to avoid large files. Not commonly used in EMAN2

LSTFAST

lsx/lst

Y

Y

Y

Y

N

Optomized version of LST

behavior is partially supported in EMAN, but be aware that it is impossible to store metadata about each image in the stack when doing this, so it is not suitable as an export format for single particle work. EMAN2 support reading of FEI MRC, which is an extended MRC format for tomography. The extra header information will be read into the header. All FEI MRC images will be 2-byte integer. ||

OMAP

omap

Y

N

Y

N

N

Also called DSN6 map, 1 byte integer per pixel

PGM

pgm

Y

Y

N

N

N

Standard graphics format with 8 bit greyscale images. No compression.

PIF

pif

Y

Y

Y

Y

N

Purdue Image Format. Images in PIF stack are homogenous. PIF doesn't currently work.

PNG

png

Y

Y

N

N

N

Excellent format for presentations. Lossless data compression, 8 bit or 16 bit per pixel

SAL

hdr/img

Y

N

N

N

N

Scans-A-Lot. Old proprietary scanner format. Separate header and data file

SITUS

situs

Y

Y

Y

N

N

Situs-specific ASCII format on a cubic lattice. Used by Situs programs

TIFF

tiff/tif

Y

Y

N

N

N

Good format for use with programs like photoshop. Some variants are good for quantitative analysis, but JPEG compression should be avoided.

V4L

v4l

Y

N

N

N

N

Used by some video-capture boards in Linux. Acquires images from the V4L2 interface in real-time(video4linux).

VTK

vtk

Y

Y

Y

N

N

Native format from Visualization Toolkit

XPLOR

xplor

Y

Y

Y

N

N

8 bytes integer, 12.5E float ASCII format

Saving EMData from Python

If you want to be prompted to supply a image name using a standard dialog use this approach 

   1 # save a single image
   2 a = test_image()
   3 from emsave import save_data
   4 save_data(a)
   5 
   6 # save a list of images as a stack
   7 b = test_image(2)
   8 save_data([a,b])

Regional I/O

Regional I/O means you can read/write a part of an image from/to a image file. This is useful when you process a huge image file on a computer with limited resource. The region specification is the same as in EMData::get_clip() function. For regional reading, you can specify a region inside an image, partially out of image bounds, or even completely out of image bounds. For regional writing, the region must be completely inside image bounds. You need be aware when reading a partially out of bounds region from HDF5 file, it will involve copying the inbound part image to the region size memory. That means there is a performance overhead for partially out bounds region reading. 

   1 # Read a origin at (1,1,1), size 8x8x8 subregion from an 64x64x64 image file 3dimage.hdf
   2 img = EMData
   3 region = Region(1,1,1,8,8,8)
   4 img.read_image("3dimage.hdf",0,False,region)

Storage type for MRC

Pixel size of image data inside EMAN2 is float. For MRC image, by default it's writed as float (4bytes/32bit). EMAN2 also support writing short (2bytes/16bit) MRC and byte (8bit) MRC. 

img = EMData(128,128)
img.write('float-image.mrc')  #by default, image will be write as float
img.write_image('short-image.mrc', 0, EMUtil.ImageType.IMAGE_MRC, False, None, EMUtil.EMDataType.EM_SHORT) #write mrc file in short (16bit)
img.write_image('byte-image.mrc', 0, EMUtil.ImageType.IMAGE_MRC, False, None, EMUtil.EMDataType.EM_UCHAR) #write mrc file in byte (8bit)

In the last write_image() funciton call, 'byte-image.mrc' is the file name you write to. Second argument, 0 is the image index in a stack. It's always 0 since MRC does not support stack. third argument, EMUtil.ImageType.IMAGE_MRC is the file type you are writing to, type 'help(EMUtil.ImageType)' in python will print out all type supported by EMAN2. forth argument, False means NOT header only. fifth argument, None means we are not doing Region I/O. sixth argument, EMUtil.EMDataType.EM_UCHAR specify the data storage type for this image file. type 'help(EMUtil.EMDataType)' will list all datatypes. For MRC, three types are supported.

EMAN2/ImageFormats (last edited 2024-02-01 04:08:01 by SteveLudtke)