Recent changes to Programs

Programs modified by jak137

jak137 — Sun, 16 Jun 2013 22:44:30 -0000

Routines modified by Anna Makal

Anna Makal — Sat, 15 Jun 2013 22:53:39 -0000

--- v8
+++ v9
@@ -30,9 +30,9 @@

 [lu__view_MonoRaysLC] - visualization of simulated lambda curves for monochromatic data ($I \sim sin(\theta)$)

-[lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)
+[lu__view_expt_clusters] - visualization of clusters experimental data (I ~ sin(theta))

-[lu_view_matrix_parameters] - visualization of orientation matrix changes (in euler angles) and cell parameters changes resulting from frame by frame matrix and cell parameters refinement
+[lu__view_matrix_parameters] - visualization of orientation matrix changes (in Euler angles) and cell parameters changes resulting from frame by frame matrix and cell parameters refinement

 ### Indexing

@@ -44,7 +44,7 @@

 [lu__hkl_assign_monolc_sph] - hkl indices assignment based on provided orientation matrices and spherical coordinate limits

-[lu_indexing2ratios_V2] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+[lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

 ##### Older versions

Routines modified by Anna Makal

Anna Makal — Sat, 15 Jun 2013 22:41:27 -0000

--- v7
+++ v8
@@ -16,7 +16,7 @@

 ##### Older versions

-[lu_hdf2spots_kruskal][https://sourceforge.net/p/laueutil/wiki/lu_hdf2spots/] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+[lu_hdf2spots_kruskal](https://sourceforge.net/p/laueutil/wiki/lu_hdf2spots/) - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

 ### Visualization

Routines modified by Anna Makal

Anna Makal — Sat, 15 Jun 2013 22:40:19 -0000

--- v6
+++ v7
@@ -16,7 +16,7 @@

 ##### Older versions

-[lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+[lu_hdf2spots_kruskal][https://sourceforge.net/p/laueutil/wiki/lu_hdf2spots/] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

 ### Visualization

Routines modified by Anna Makal

Anna Makal — Wed, 12 Jun 2013 22:17:27 -0000

--- v5
+++ v6
@@ -32,7 +32,7 @@

 [lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)

-[lu_view_matrix_parameters] - 
+[lu_view_matrix_parameters] - visualization of orientation matrix changes (in euler angles) and cell parameters changes resulting from frame by frame matrix and cell parameters refinement

 ### Indexing

Routines modified by Anna Makal

Anna Makal — Wed, 12 Jun 2013 19:00:02 -0000

--- v4
+++ v5
@@ -54,6 +54,8 @@

 [lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

+[lu__match_pairs_V4] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+
 ## Post-Precognition data processing

 [lu_dump_pc_cell] - combines parameters stored in _.inp_ Precognition output files into single file suitable for statistical analysis

Routines modified by Anna Makal

Anna Makal — Tue, 11 Jun 2013 16:50:50 -0000

--- v3
+++ v4
@@ -20,7 +20,9 @@

 ### Visualization

-[lu__view_correlation_ratios] - produces correlation plots for unindexed ratio
+[lu__view_correlation_ratios] - produces correlation plots for unindexed ratios
+
+[lu__view_correlation_merged_ratios] - produces correlation plots for indexed and merged ratios

 [lu__view_mda] - visualization of experimental lambda curve

@@ -30,19 +32,19 @@

 [lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)

+[lu_view_matrix_parameters] - 
+
 ### Indexing

 [lu__match_pairs] - orientation matrix calculation based on automatic cluster searches

+[lu__refine_orientmatrix] - orientation matrix and cell parameter refinement on frame by frame basis

+[lu__hkl_assign_monolc] - hkl indices assignment based on provided orientation matrices and eulerian coordinate limits

+[lu__hkl_assign_monolc_sph] - hkl indices assignment based on provided orientation matrices and spherical coordinate limits

-[lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
-## Post-Precognition data processing
-
-[lu_dump_pc_cell] - combines parameters stored in _.inp_ Precognition output files into single file suitable for statistical analysis
-
-[lu_respt2expt] - combines the information from _re.spt_ Precognition output files into single HDF5 file for indexing input
+[lu_indexing2ratios_V2] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

 ##### Older versions

@@ -51,6 +53,12 @@
 [lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix

 [lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+
+## Post-Precognition data processing
+
+[lu_dump_pc_cell] - combines parameters stored in _.inp_ Precognition output files into single file suitable for statistical analysis
+
+[lu_respt2expt] - combines the information from _re.spt_ Precognition output files into single HDF5 file for indexing input

 ### Post-`LaueGui` ratio processing

Routines modified by Anna Makal

Anna Makal — Tue, 11 Jun 2013 16:34:28 -0000

--- v2
+++ v3
@@ -1,22 +1,24 @@
-# Programs
+## Programs

-## Pre-Indexing and Integration pipeline
+### Pre-Indexing and Integration pipeline

 [lu_mccd2hdf] - stores images and `LaueCollect` information in a single HDF5 file

-[lu_hdf2spots] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
-
-[lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+[lu_hdf2spots] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical test for laser datasets

 [lu_spots2ratios] - calculates ratios from integrated but unindexed data for consistency analysis

 [lu_ratios2averaging] - averages ratios from integrated but unindexed data over the similar position on a given frame

-[lu_spots2expt] - combines the information on integrated spots and detector geometry into indexing input
+[lu_spots2expt] - combines the information on integrated spots and detector characteristics & geometry into indexing input

 [lu_fcf2mono] - stores information on monochromatic data in HDF5 file for indexing input

-## Visualization
+##### Older versions
+
+[lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+
+### Visualization

 [lu__view_correlation_ratios] - produces correlation plots for unindexed ratio

@@ -28,15 +30,12 @@

 [lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)

-## Indexing
-
-[lu__indexing2cm] - orientation matrix calculation by-hand assignment of hkl indices to experimental data
+### Indexing

 [lu__match_pairs] - orientation matrix calculation based on automatic cluster searches

-[lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix

-[lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+

 [lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
 ## Post-Precognition data processing
@@ -45,18 +44,21 @@

 [lu_respt2expt] - combines the information from _re.spt_ Precognition output files into single HDF5 file for indexing input

-## Post-`LaueGui` ratio processing
+##### Older versions
+
+[lu__indexing2cm] - orientation matrix calculation by-hand assignment of hkl indices to experimental data
+
+[lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix
+
+[lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+
+### Post-`LaueGui` ratio processing

 [lu_ratios] - calculates average ratios over series of ON and OFF frames

 [lu_plot_r_vs_r] - given a couple of merged _hkl_ files searches for common hkl indices and prepares input for correlation plot

-## Miscallenous
+### Miscallenous

 [lu_fco_2_random_ratios_hkl] - generates random ratios with a given gaussian distribution

-# Installation
-
-Python distribution that contain all of the required dependencies (numpy, scipy, vtk, h5py, wx, matplotlib and several modules from enthought suite: traits, traits.ui, tvtk):
-* [Enthought Python Distribution](http://www.enthought.com/products/epd.php) (commercial but free for academics)
-* [Python(x,y)](http://www.pythonxy.com) (Windows XP/Vista/7 32bits only)

Routines modified by Anna Makal

Anna Makal — Tue, 11 Jun 2013 16:28:12 -0000

--- v1
+++ v2
@@ -2,58 +2,58 @@

 ## Pre-Indexing and Integration pipeline

-[wiki:lumccd2hdf lu_mccd2hdf] - stores images and `LaueCollect` information in a single HDF5 file
+[lu_mccd2hdf] - stores images and `LaueCollect` information in a single HDF5 file

-[wiki:luhdf2spots lu_hdf2spots] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+[lu_hdf2spots] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

-[wiki:luhdf2spotskruskal lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets
+[lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

-[wiki:luspots2ratios lu_spots2ratios] - calculates ratios from integrated but unindexed data for consistency analysis
+[lu_spots2ratios] - calculates ratios from integrated but unindexed data for consistency analysis

-[wiki:luratios2averaging lu_ratios2averaging] - averages ratios from integrated but unindexed data over the similar position on a given frame
+[lu_ratios2averaging] - averages ratios from integrated but unindexed data over the similar position on a given frame

-[wiki:luspots2expt lu_spots2expt] - combines the information on integrated spots and detector geometry into indexing input
+[lu_spots2expt] - combines the information on integrated spots and detector geometry into indexing input

-[wiki:lufcf2mono lu_fcf2mono] - stores information on monochromatic data in HDF5 file for indexing input
+[lu_fcf2mono] - stores information on monochromatic data in HDF5 file for indexing input

 ## Visualization

-[wiki:lucorrelation lu__view_correlation_ratios] - produces correlation plots for unindexed ratio
+[lu__view_correlation_ratios] - produces correlation plots for unindexed ratio

-[wiki:luviewmda lu__view_mda] - visualization of experimental lambda curve
+[lu__view_mda] - visualization of experimental lambda curve

-[wiki:luviewmonox lu__view_mono_x] - visualization of symmetry-expanded monochromatic data in a projection on a sphere
+[lu__view_mono_x] - visualization of symmetry-expanded monochromatic data in a projection on a sphere

-[wiki:luviewmonorays lu__view_MonoRaysLC] - visualization of simulated lambda curves for monochromatic data ($I \sim sin(\theta)$)
+[lu__view_MonoRaysLC] - visualization of simulated lambda curves for monochromatic data ($I \sim sin(\theta)$)

-[wiki:luviewexptclusters lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)
+[lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)

 ## Indexing

-[wiki:luindexing2cm lu__indexing2cm] - orientation matrix calculation by-hand assignment of hkl indices to experimental data
+[lu__indexing2cm] - orientation matrix calculation by-hand assignment of hkl indices to experimental data

-[wiki:lumatchpairs lu__match_pairs] - orientation matrix calculation based on automatic cluster searches
+[lu__match_pairs] - orientation matrix calculation based on automatic cluster searches

-[wiki:luassignmono lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix
+[lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix

-[wiki:lumatchpairsV4 lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+[lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

-[wiki:luindexing2ratios lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
+[lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment
 ## Post-Precognition data processing

-[wiki:ludumppc lu_dump_pc_cell] - combines parameters stored in _.inp_ Precognition output files into single file suitable for statistical analysis
+[lu_dump_pc_cell] - combines parameters stored in _.inp_ Precognition output files into single file suitable for statistical analysis

-[wiki:lurespt lu_respt2expt] - combines the information from _re.spt_ Precognition output files into single HDF5 file for indexing input
+[lu_respt2expt] - combines the information from _re.spt_ Precognition output files into single HDF5 file for indexing input

 ## Post-`LaueGui` ratio processing

-[wiki:luratios lu_ratios] - calculates average ratios over series of ON and OFF frames
+[lu_ratios] - calculates average ratios over series of ON and OFF frames

-[wiki:luplotrvsr lu_plot_r_vs_r] - given a couple of merged _hkl_ files searches for common hkl indices and prepares input for correlation plot
+[lu_plot_r_vs_r] - given a couple of merged _hkl_ files searches for common hkl indices and prepares input for correlation plot

 ## Miscallenous

-[wiki:lurandomratios lu_fco_2_random_ratios_hkl] - generates random ratios with a given gaussian distribution
+[lu_fco_2_random_ratios_hkl] - generates random ratios with a given gaussian distribution

 # Installation

Routines modified by Anna Makal

Anna Makal — Mon, 10 Jun 2013 16:09:26 -0000

Programs

Pre-Indexing and Integration pipeline

[wiki:lumccd2hdf lu_mccd2hdf] - stores images and LaueCollect information in a single HDF5 file

[wiki:luhdf2spots lu_hdf2spots] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

[wiki:luhdf2spotskruskal lu_hdf2spots_kruskal] - calculates frame statistics, masks, finds spot location and background-corrected integrated intensities with optional use of Kruskall-Wallis statistical tes for laser datasets

[wiki:luspots2ratios lu_spots2ratios] - calculates ratios from integrated but unindexed data for consistency analysis

[wiki:luratios2averaging lu_ratios2averaging] - averages ratios from integrated but unindexed data over the similar position on a given frame

[wiki:luspots2expt lu_spots2expt] - combines the information on integrated spots and detector geometry into indexing input

[wiki:lufcf2mono lu_fcf2mono] - stores information on monochromatic data in HDF5 file for indexing input

Visualization

[wiki:lucorrelation lu__view_correlation_ratios] - produces correlation plots for unindexed ratio

[wiki:luviewmda lu__view_mda] - visualization of experimental lambda curve

[wiki:luviewmonox lu__view_mono_x] - visualization of symmetry-expanded monochromatic data in a projection on a sphere

[wiki:luviewmonorays lu__view_MonoRaysLC] - visualization of simulated lambda curves for monochromatic data ($I \sim sin(\theta)$)

[wiki:luviewexptclusters lu__view_expt_clusters] - visualization of clusters experimental data ($I \sim sin(\theta)$)

Indexing

[wiki:luindexing2cm lu__indexing2cm] - orientation matrix calculation by-hand assignment of hkl indices to experimental data

[wiki:lumatchpairs lu__match_pairs] - orientation matrix calculation based on automatic cluster searches

[wiki:luassignmono lu__hkl_assign_monolc] - assignment of hkl indices to experimental data based on a given orientation matrix

[wiki:lumatchpairsV4 lu__match_pairs_indexing] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

[wiki:luindexing2ratios lu_indexing2ratios] - orientation matrix calculation based on automatic cluster searches merged with hkl assignment

Post-Precognition data processing

[wiki:ludumppc lu_dump_pc_cell] - combines parameters stored in .inp Precognition output files into single file suitable for statistical analysis

[wiki:lurespt lu_respt2expt] - combines the information from re.spt Precognition output files into single HDF5 file for indexing input

Post-`LaueGui` ratio processing

[wiki:luratios lu_ratios] - calculates average ratios over series of ON and OFF frames

[wiki:luplotrvsr lu_plot_r_vs_r] - given a couple of merged hkl files searches for common hkl indices and prepares input for correlation plot

Miscallenous

[wiki:lurandomratios lu_fco_2_random_ratios_hkl] - generates random ratios with a given gaussian distribution

Installation

Python distribution that contain all of the required dependencies (numpy, scipy, vtk, h5py, wx, matplotlib and several modules from enthought suite: traits, traits.ui, tvtk):
Enthought Python Distribution (commercial but free for academics)
Python(x,y) (Windows XP/Vista/7 32bits only)

Recent changes to Programs

Programs modified by jak137

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Routines modified by Anna Makal

Programs

Pre-Indexing and Integration pipeline

Visualization

Indexing

Post-Precognition data processing

Post-LaueGui ratio processing

Miscallenous

Installation

Post-`LaueGui` ratio processing