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Deletions are marked like this. Additions are marked like this.
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||Type ||Extension ||Read ||Write ||3D ||stack ||Comments ||
||HDF5 ||hdf ||Y ||Y ||Y ||Y ||This is the only format supporting the full metadata model used in EMAN2. That is, this is the only format you can export data from the database into and preserve all of the information about each image. Technically it can also support different sized images in the same stack, though this behavior is not normally used. ||
||MRC ||mrc ||Y ||Y ||Y ||N || Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This 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.||
||Spider ||spi ||Y ||Y ||Y ||Y ||To read the overall image header in a stacked spider file, use image_index = -1. ||
||Imagic ||img/hed ||Y ||Y ||Y ||Y ||seperate header and data file, cannot store multiple 3D images in one file ||
||DM3 ||dm3 ||Y ||N ||N ||N || ||
||TIFF ||tiff/tif ||Y ||Y ||N ||N ||8bit or 16bit per pixel ||
||PGM ||pgm ||Y ||Y ||N ||N ||8 bits per pixel ||
||PIF ||pif ||Y ||Y ||Y ||Y ||images in PIF stack are homogenous. PIF doesn't currently work. ||
||VTK ||vtk ||Y ||Y ||Y ||N || ||
||PNG ||png ||Y ||Y ||N ||N ||lossless data compression, 8 bit or 16 bit per pixel ||
||SAL ||hdr/img ||Y ||N ||N ||N ||seperate header and data file ||
||ICOS ||icos ||Y ||Y ||Y ||N || ||
||EMIM ||emim ||Y ||N ||Y ||Y ||images in stack are homogenous ||
||Gatan2 ||dm2 ||Y ||N ||N ||N || ||
||Amira ||am ||Y ||Y ||Y ||N || ||
||XPLOR ||xplor ||Y ||Y ||Y ||N ||8 bytes integer, 12.5E float format ||
||EM ||em ||Y ||Y ||Y ||N || ||
||V4L ||v4l ||Y ||N ||N ||N ||Acquires images from the V4L2 interface in real-time(video4linux). ||
||JPEG ||jpg/jpeg ||N ||Y ||N ||N ||lossy data compression ||
||FITS ||fts ||Y ||N ||Y ||N ||common file format in astronomy ||
||LST ||lst ||Y ||Y ||Y ||Y ||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 ||Optomized version of LST||		 ||Type ||Extension ||Read ||Write ||3D ||stack ||Regional I/O ||Comments ||
||HDF5 ||hdf ||Y ||Y ||Y ||Y ||Y ||This is the only format supporting the full metadata model used in EMAN2. That is, this is the only format you can export data from the database into and preserve all of the information about each image. Technically it can also support different sized images in the same stack, though this behavior is not normally used. ||
||MRC ||mrc ||Y ||Y ||Y ||N ||Y ||Note that some programs will treat 3D MRC files as stacks of 2D imagess (like IMOD). This 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. ||
||Spider ||spi ||Y ||Y ||Y ||Y ||Y ||To read the overall image header in a stacked spider file, use image_index = -1. ||
||Imagic ||img/hed ||Y ||Y ||Y ||Y ||Y ||seperate header and data file, cannot store multiple 3D images in one file. Regional I/O is only available for 2D. ||
||DM3 ||dm3 ||Y ||N ||N ||N ||N || ||
||TIFF ||tiff/tif ||Y ||Y ||N ||N ||N ||8bit or 16bit per pixel ||
||PGM ||pgm ||Y ||Y ||N ||N ||N ||8 bits per pixel ||
||PIF ||pif ||Y ||Y ||Y ||Y ||N ||images in PIF stack are homogenous. PIF doesn't currently work. ||
||VTK ||vtk ||Y ||Y ||Y ||N ||N || ||
||PNG ||png ||Y ||Y ||N ||N ||N ||lossless data compression, 8 bit or 16 bit per pixel ||
||SAL ||hdr/img ||Y ||N ||N ||N ||N ||seperate header and data file ||
||ICOS ||icos ||Y ||Y ||Y ||N ||Y || ||
||EMIM ||emim ||Y ||N ||Y ||Y ||N ||images in stack are homogenous ||
||Gatan2 ||dm2 ||Y ||N ||N ||N ||N || ||
||Amira ||am ||Y ||Y ||Y ||N ||N || ||
||XPLOR ||xplor ||Y ||Y ||Y ||N ||N ||8 bytes integer, 12.5E float format ||
||EM ||em ||Y ||Y ||Y ||N ||Y || ||
||V4L ||v4l ||Y ||N ||N ||N ||N ||Acquires images from the V4L2 interface in real-time(video4linux). ||
||JPEG ||jpg/jpeg ||N ||Y ||N ||N ||N ||lossy data compression ||
||FITS ||fts ||Y ||N ||Y ||N ||N ||common file format in astronomy ||
||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 ||
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= 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.

{{{#!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)

}}}

Contents

  1. Table of supported image formats in EMAN2
  2. Saving EMData from Python
  3. Regional I/O

Table of supported image formats in EMAN2

Type

Extension

Read

Write

3D

stack

Regional I/O

Comments

HDF5

hdf

Y

Y

Y

Y

Y

This is the only format supporting the full metadata model used in EMAN2. That is, this is the only format you can export data from the database into and preserve all of the information about each image. Technically it can also support different sized images in the same stack, though this behavior is not normally used.

MRC

mrc

Y

Y

Y

N

Y

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

Spider

spi

Y

Y

Y

Y

Y

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

Imagic

img/hed

Y

Y

Y

Y

Y

seperate header and data file, cannot store multiple 3D images in one file. Regional I/O is only available for 2D.

DM3

dm3

Y

N

N

N

N

TIFF

tiff/tif

Y

Y

N

N

N

8bit or 16bit per pixel

PGM

pgm

Y

Y

N

N

N

8 bits per pixel

PIF

pif

Y

Y

Y

Y

N

images in PIF stack are homogenous. PIF doesn't currently work.

VTK

vtk

Y

Y

Y

N

N

PNG

png

Y

Y

N

N

N

lossless data compression, 8 bit or 16 bit per pixel

SAL

hdr/img

Y

N

N

N

N

seperate header and data file

ICOS

icos

Y

Y

Y

N

Y

EMIM

emim

Y

N

Y

Y

N

images in stack are homogenous

Gatan2

dm2

Y

N

N

N

N

Amira

am

Y

Y

Y

N

N

XPLOR

xplor

Y

Y

Y

N

N

8 bytes integer, 12.5E float format

EM

em

Y

Y

Y

N

Y

V4L

v4l

Y

N

N

N

N

Acquires images from the V4L2 interface in real-time(video4linux).

JPEG

jpg/jpeg

N

Y

N

N

N

lossy data compression

FITS

fts

Y

N

Y

N

N

common file format in astronomy

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

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. 

   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)

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