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Contents
Contents
Diffraction Microscopy reconstruction software
Contents
List of Tables
List of Figures
Getting started
Updating this document
General remarks
Complete programs, and subroutine libraries
Subroutine library coding conventions
The file
dm.h
#define
s: system-level, and our own ``invented'' ones
Array memory allocation
Array ordering and centering conventions
Complex arrays
Using the predefined array structures
Testing your implementation of the subroutine libraries
Data files
Reading and writing ALS 9.0.1
.nc
files
Routines for reading and writing
.nc
files in C/C++
Routines for reading and writing
.nc
files in IDL
HDF 5 files involved in iterative reconstructions
General structure of our HDF 5 files
The assembled diffraction intensity group
"/adi"
Data error factor in the
"/adi"
group
Assembled diffraction sequence
"/ads"
group
Assembly info
"/ainfo"
group
Support mask
"/spt"
group
Iterate amplitude
"/itn"
group
3D data assembly
.3da
files
The subroutine library
dm_fileio.c
Creating an
.h5
file and accessing an existing file
Reading and writing/updating the
"/comments"
group in
C
Reading and writing the
"/adi"
group in
C
Reading and writing the
"/comments"
group in
C
Reading and writing the
"/ainfo"
group in
C
Reading and writing the
"/spt"
group in
C
Reading and writing the
"/itn"
group in
C
IDL routines for file I/O
Reading and writing the
"/ainfo"
group in
IDL
Procedures for diffraction data analysis
Cataloging files: the routine
dt_list_series.pro
Merging individual ALS 9.0.1 exposures for one 2D view: Henry Chapman's
merger
Using
merger_manager
Wish list for enhancements to
merger
Merging individual ALS 9.0.1 exposures for one 2D view:
commie
A word on the
commie
distribution
Quick start: Assembly file
Quick start: Command line arguments (CLAs)
Quick start: Program flow
Further information
From 2D to 3D data: Anton Barty's program
Xewald
Execution
Using
Output
Wish list for enhancements to
Xewald
Ideas for programs we should have
Cewald
: a C program for 3D data assembly
Estimating the center of a diffraction pattern
Estimating information content in a 2D view
Characterizing noise
Masking the beamstop and detecting saturated pixels
Displaying autocorrelation function from subregions of the diffraction data array
Estimating support from the autocorrelation
Iterative phasing programs
Pierre Thibault's
retriever
Anton Barty's 3dmpi
Wishlist for 3dmpi
Wishlist for reconstruction programs
Application of Fourier modulus constraint with error factor per pixel
Application of support constraint
Calculation of the next iterate
Calculation
at a particular iterate
Calculation of error metric at a particular iterate
Script language for running iterations
Structure outside the support
Visualization of results
Routines for making movies of iterates
Routines for viewing 3D data
The array calculation subroutine library
dm_array.c
MPI-enabled FFTs
Working with FFTW 2.1.5 MPI
Working with
dist_fft
FFTs using
dm_array_fft()
A roadmap for work at Stony Brook
Running MPI code
Running code using LAM MPI on Stony Brook's Apple cluster
Things to set up just once
Running your code
Running
dist_fft_test
using MPICH
Running MPICH code on a subset of the cluster
Running MPI DIST_FFT
Compiler
Header file modification
About this document ...
Microscope User 2008-11-25
