From c3fd9eb6fdedecb49a765ed96e8da8cab3bb2fc0 Mon Sep 17 00:00:00 2001
From: Laura Nervo <lnervo@esrf.fr>
Date: Tue, 28 Aug 2012 09:01:24 +0000
Subject: [PATCH] Old and general formatting in the code...
Signed-off-by: Laura Nervo <laura.nervo@esrf.fr>
git-svn-id: https://svn.code.sf.net/p/dct/code/trunk@695 4c865b51-4357-4376-afb4-474e03ccb993
---
5_reconstruction/gtFsimCheckMissingGrains.m | 17 ++--
6_rendering/gtRenderGrains | 34 -------
zUtil_Help/gtStatus.m | 101 ++++++++++----------
3 files changed, 61 insertions(+), 91 deletions(-)
delete mode 100755 6_rendering/gtRenderGrains
diff --git a/5_reconstruction/gtFsimCheckMissingGrains.m b/5_reconstruction/gtFsimCheckMissingGrains.m
index e35b5ba4..9f88a09b 100644
--- a/5_reconstruction/gtFsimCheckMissingGrains.m
+++ b/5_reconstruction/gtFsimCheckMissingGrains.m
@@ -16,15 +16,16 @@ function missing = gtFsimCheckMissingGrains(phase_num)
% get number of jobs for that functions from OAR
arrays=logviewOar('gtForwardSimulate_v2',[],false);
-if ~isempty(arrays.fname)
-if ~isempty(arrays.('gtForwardSimulate_v2').logs)
- filename = arrays.('gtForwardSimulate_v2').logs;
- [~,njobs] = unix(['grep "njobs" ' filename ' | awk -F" = " ''{print $2}''']);
- nof_jobs = str2double(njobs);
-end
-else
+% if ~isempty(arrays.fname)
+% if ~isempty(arrays.('gtForwardSimulate_v2').logs)
+% filename = arrays.('gtForwardSimulate_v2').logs;
+% [~,njobs] = unix(['grep "njobs" ' filename ' | awk -F" = " ''{print $2}''']);
+% nof_jobs = str2double(njobs);
+% end
+% else
nof_jobs = 1;
-end
+
+% end
% get last gtForwardSimulate_v2 run date from oar.log file
o=fileread('oar.log');
diff --git a/6_rendering/gtRenderGrains b/6_rendering/gtRenderGrains
deleted file mode 100755
index e0b558e3..00000000
--- a/6_rendering/gtRenderGrains
+++ /dev/null
@@ -1,34 +0,0 @@
-subvol=grains(1:2:end, 1:2:end, 30:2:250);
-
-
-map=gtRodriguezColormap(r_vectors);
-
-list=unique(subvol(:,:,50));
-
-
-list(find(list==0))=[];%don't render the background
-
-figure;
-%go through graini by grain
-for i=1:length(list)
- disp(sprintf('rendering grain %d of %d...', i, length(list)))
-
- voltest=zeros(size(subvol));
-
- voltest(find(subvol==list(i)))=1;
- %pad for smoothing
- voltest2=zeros(size(voltest)+10);
- voltest2(6:end-5, 6:end-5, 6:end-5)=voltest;
- voltest2=smooth3(voltest2, 'box', 3);
- p(i)=patch(isosurface(voltest2, 0.5));
- %set colour according to map (note map(1,:)=[0 0 0] for background, so +1
- set(p(i), 'FaceColor', map(list(i)+1, :), 'EdgeColor', 'none');
-
-end
-camlight
-lighting phong
-axis equal
-axis vis3d
-set(gca, 'xTick', []);
-set(gca, 'yTick', []);
-set(gca, 'zTick', []);
diff --git a/zUtil_Help/gtStatus.m b/zUtil_Help/gtStatus.m
index 4e2e831e..f129f328 100644
--- a/zUtil_Help/gtStatus.m
+++ b/zUtil_Help/gtStatus.m
@@ -1,30 +1,31 @@
-
-
function gtStatus()
-
-
-% check status of a dataset, show progress where possible, and tell a user
-% where one might have a problem.
-
-% to add - prompts
-% to add - look into most recent OAR stats to get more info
-
+% GTSTATUS Checks the status of a dataset, show progress where possible
+% and tell a user where one might have a problem.
+% gtStatus()
+% ----------
+% to add - prompts
+% - look into most recent OAR stats to get more info
+%
+% Version 001.2 23/08/2012 by LNervo
+% Code formatting
+%
+% Version 001 by AKing
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% FIRST THINGS FIRST - PARAMETERS FILE
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% is there a parameters file?
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
if exist('parameters.mat', 'file')
load parameters
fprintf('Found a parameters file...\n')
fprintf('Dataset name is %s\n', parameters.acq.name)
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
else
fprintf('No parameters.mat file found! Are you in the analysis directory?\n')
a=pwd;
fprintf('Current directory is: %s\n', a)
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
return
end
@@ -69,7 +70,7 @@ if exist('oar.log', 'file')
ndx=ndx+81;
end
launch_time=status((end-30):(end-12));
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
fprintf('Last OAR job was %s \n(array %d launched at %s) \n', lastoar_name, lastoar_array, launch_time)
% finished?
@@ -93,7 +94,7 @@ else
fprintf('No oar.log file found... \n')
fprintf('Possible OAR problem? \n')
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -121,14 +122,15 @@ disp('checking what images are present')
% make the first check on the full images. If these are not all present,
% look into the other images to see what is missing:
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
-d=dir(fullfile(parameters.acq.dir,'1_preprocessing/full', 'full*.edf'));
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+d=dir(fullfile(parameters.acq.dir,'1_preprocessing','full', 'full*.edf'));
nfull=length(d);
fprintf('found %d full images out of %d expected\n', nfull, totproj)
if nfull~=totproj
problem_list{end+1}='missing full images : possible gtCreateFullLive problem';
end
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
% was preprocessing successful?
if nfull==totproj
preprocessing_ok=true;
@@ -137,30 +139,30 @@ else
fprintf('Checking raw, corrected and preprocessed images')
- %% Orig images
- d=dir(fullfile(parameters.acq.dir,'0_rawdata/Orig', [parameters.acq.name '*.edf']));
+ % Orig images
+ d=dir(fullfile(parameters.acq.dir,'0_rawdata','Orig', [parameters.acq.name '*.edf']));
n_orig=length(d);
fprintf('found %d raw images out of %d expected\n', n_orig, totproj)
if n_orig<totproj
problem_list{end+1}='missing raw images: possible gtCopyCorrectUndistortCondor problem';
end
- d=dir(fullfile(parameters.acq.dir,'0_rawdata/Orig', 'ref*_*.edf'));
+ d=dir(fullfile(parameters.acq.dir,'0_rawdata','Orig', 'ref*_*.edf'));
nref_orig=length(d);
fprintf('found %d raw references out of %d expected\n', nref_orig, totref)
if nref_orig~=totref
problem_list{end+1}='missing raw reference images: possible gtCopyCorrectUndistortCondor problem';
end
- d=dir(fullfile(parameters.acq.dir,'0_rawdata/Orig', 'dark*.edf'));
- if length(d)>0
+ d=dir(fullfile(parameters.acq.dir,'0_rawdata','Orig', 'dark*.edf'));
+ if ~isempty(d)
fprintf('found at least one dark images\n')
else
fprintf('No raw dark image found\n')
problem_list{end+1}='missing raw dark image: possible gtCopyCorrectUndistortCondor problem';
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
-
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
- %% Treated images
+ % Treated images
d=dir(fullfile(parameters.acq.dir,'0_rawdata', parameters.acq.name, [parameters.acq.name '*.edf']));
n_copy=length(d);
fprintf('found %d copied images out of %d expected\n', n_copy, totproj)
@@ -180,16 +182,16 @@ else
if ndark_copy>0
fprintf('found at least one copied dark images\n')
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
-
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
% was copying successful?
- if n_copy>=totproj & nref_copy==nref_copy & ndark_copy>0
+ if n_copy>=totproj && nref_copy==nref_copy && ndark_copy>0
copy_ok=true;
end
- %% Preprocessed images
+ % Preprocessed images
disp('checking for other preprocessed images...')
d=dir(fullfile(parameters.acq.dir,'0_rawdata', parameters.acq.name, 'refHST*.edf'));
nrefHST=length(d);
@@ -226,12 +228,13 @@ end % if full images present
% SEGMENTATION STATUS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp('Connecting to database to check segmentation...')
-gtDBConnect;
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+gtDBConnect();
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+
if strcmp(parameters.seg.method, 'doublethr')
fprintf('Segmentation method: Double threshold \n')
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
% seed segmentation status
cmd=sprintf('select count(*) from %sfullmedianvals', parameters.acq.name);
@@ -243,7 +246,7 @@ if strcmp(parameters.seg.method, 'doublethr')
if n_fmv~=n_fmv_finished
problem_list{end+1}='gtSeedSegmentation_doublethr has not finished';
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
% blob segmentation progress
@@ -259,10 +262,10 @@ if strcmp(parameters.seg.method, 'doublethr')
fprintf('Segmentation has treated %d out of %d seeds\n',done_seeds, tot_seeds)
fprintf('Segmentation has found %d blobs\n', n_blobs')
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
% was segmentation successful?
- if done_seeds==tot_seeds & n_blobs>1
+ if done_seeds==tot_seeds && n_blobs>1
blobs_ok=true;
end
@@ -270,11 +273,11 @@ if strcmp(parameters.seg.method, 'doublethr')
elseif strcmp(parameters.seg.method, 'singlethr')
fprintf('Segmentation method: Single threshold \n')
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
n_blobs=sprintf('select count(*) from %sdifblob', parameters.acq.name);
fprintf('Segmentation has found %d blobs\n',n_blobs)
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
% was segmentation successful?
if nblobs>1
@@ -288,7 +291,7 @@ end
cmd=sprintf('select count(*) from %sdifspot', parameters.acq.name);
n_spots=mym(cmd);
fprintf('Database has %d difspots from %d blobs\n',n_spots, n_blobs)
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% PAIRMATCHING STATUS
@@ -304,7 +307,7 @@ end
fprintf('Database has %d spot pairs for phase %d from %d difspots (%0.1f%% matching) \n'...
,n_pairs(ii), ii, n_spots,pair_percentage )
end
-fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% INDEXING STATUS
@@ -318,7 +321,7 @@ for ii=length(parameters.cryst)
fprintf('This file was created %s \n', d.date)
n_pairs_inp(ii)=length(inp.tot.pairid);
if n_pairs_inp(ii)~=n_pairs(ii)
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
fprintf('!!! Strong warning !!! \n')
fprintf('Number of pairs in the indexing input file does not match the spotpair table\n')
fprintf('If you have update the pair matching, un-check "use input file" in gtSetupIndexing\n')
@@ -330,7 +333,7 @@ for ii=length(parameters.cryst)
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
% is there an output file?
d2=dir(sprintf('4_grains/phase_%02d/index.mat', ii));
@@ -343,12 +346,12 @@ for ii=length(parameters.cryst)
else
fprintf('No indexing output found for phase %02d\n', ii)
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
if d.datenum>d2.datenum
fprintf('!!! Strong warning !!! \n')
fprintf('Input file is newer than the output file! Indexing has started but not been finished\n')
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
end
end
@@ -369,7 +372,7 @@ for ii=1:length(parameters.cryst)
end
end
-check=inputwdefault('use gtFsimCheckMissingGrains to check forward sim output?', 'n')
+check=inputwdefault('use gtFsimCheckMissingGrains to check forward sim output?', 'n');
if strcmpi(check, 'y')
for ii=length(parameters.cryst)
fprintf('Check forward simulation for phase %02d:\n', ii)
@@ -381,7 +384,7 @@ for ii=length(parameters.cryst)
fprintf('These grains failed:\n')
list.ind
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
end
end
@@ -395,7 +398,7 @@ for ii=length(parameters.cryst)
if exist(sprintf('4_grains/phase_%02d/index.mat', ii), 'file')
a=load(sprintf('4_grains/phase_%02d/index.mat', ii));
check=zeros(length(a.grain), 2);
- warning('off') % hide warning messages
+ warning('off','Warning OFF') % hide warning messages
for jj=1:length(a.grain)
fprintf('%04d/%04d', jj, length(a.grain));
b=load(sprintf('4_grains/phase_%02d/grain_%04d.mat', ii, jj), 'vol', 'seg');
@@ -424,8 +427,8 @@ for ii=length(parameters.cryst)
fprintf('\nno indexter output found\n')
end
- fprintf('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n')
- warning('on') % hide warning messages
+ disp('%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%')
+ warning('on','Warning ON') % hide warning messages
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
--
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