diff --git a/2_difspot/gtReadAndThreshold.m b/2_difspot/gtReadAndThreshold.m
new file mode 100644
index 0000000000000000000000000000000000000000..bf0946ccdfc3a33c3008951fa17f54885925b245
--- /dev/null
+++ b/2_difspot/gtReadAndThreshold.m
@@ -0,0 +1,99 @@
+function [img, med_value, info] = gtReadAndThreshold(ndx, parameters, thr_single, nodisp, info)
+% GTREADANDTHRESHOLD Reads the full image with number 'ndx' and thresholds
+% it. It can also return the median value of the full image.
+%
+% It sets the image to zero inside the segmentation bounding box
+% (parameters.seg.bbox) and outside where it is under the threshold.
+% Can subtract the remaining median background of the full image
+% (calculated and applied outside seg.bbox).
+% Thresholds to seg.thr_single by default, or allow another threshold
+% value to be passed in. Pass in NaN to return the greyscale image without
+% thresholding.
+%
+% INPUT
+% ndx - full image number to be read
+% parameters.
+% prep.correct_drift
+% prep.correct_drift_iteration
+%
+% seg.thr_single - the threshold value to be applied
+% seg.bbox - bounding box of area omitted in segmentation
+% seg.background_subtract - if true, the full image's median will be
+% offset to zero
+%
+% Optional INPUT
+% thr_single - threshold value that overrides seg.thr_single;
+% if NaN, no thresholding is done
+% nodisp - if true, no text will be displayed
+% info - EDF header structure
+%
+% OUTPUT
+% im - segmented image
+% med_value - median value of the full image
+% info - EDF header structure
+%
+% [img, med_value, info] = gtReadAndThreshold(ndx, parameters, thr_single, nodisp, info)
+%
+%
+% Version 002 08-05-2012 by P.Reischig
+% Updated to new parameters (thr_single) and cleaned.
+%
+% Modified by Nicola Vigano', 2012, nicola.vigano@esrf.fr
+% Changed gtPlaceSubImage -> gtPlaceSubImage2, added EDF header recycling.
+%
+
+ seg = parameters.seg;
+ prep = parameters.prep;
+
+ % if a threshold other than th2 is passed in
+ if (~exist('thr_single', 'var'))
+ thr_single = seg.thr_single;
+ end
+ if (~exist('nodisp', 'var'))
+ nodisp = false;
+ end
+ out = GtConditionalOutput(~nodisp);
+
+ % should we wait for images to be shifted by gtApplyDrifts?
+ waitfortranslated = false;
+
+ if isfield(prep, 'correct_drift') && strcmp(prep.correct_drift, 'required')
+ waitfortranslated = prep.correct_drift_iteration;
+ end
+
+ fname = sprintf('1_preprocessing/full/full%04d.edf', ndx);
+
+ out.fprintf('now processing image %s\n', fname);
+
+ if (~exist('info', 'var') || isempty(info))
+ [im_full, info] = edf_wait_read(fname, [], waitfortranslated);
+ else
+ [im_full, info] = edf_wait_read(fname, [], waitfortranslated, info);
+ end
+
+ % would be very easy to add this as an option in gtCreateFullLive - do
+ % it once there and then not again...
+ if (isfield(seg, 'background_subtract') && (seg.background_subtract == true))
+ %subtract the median of the background
+ %taken from gtFullStatCondor - thanks Peter!
+ nullbb = NaN(seg.bbox(4), seg.bbox(3));
+ imn = gtPlaceSubImage2(nullbb, im_full, seg.bbox(1), seg.bbox(2));
+ imn = imn(~isnan(imn(:)));
+
+ med_value = median(imn);
+ im_full = im_full - med_value;
+
+ out.fprintf('subtracting median background value\n');
+ else
+ med_value = NaN;
+ end
+
+ % now blank out the extinction image in the centre
+ img = gtPlaceSubImage2( zeros(seg.bbox(4), seg.bbox(3)), im_full, ...
+ seg.bbox(1), seg.bbox(2));
+
+ % do the thresholding
+ if ~isnan(thr_single)
+ img(img < thr_single) = 0;
+ end
+end
diff --git a/2_difspot/gtSeedThreshold_doublethr.m b/2_difspot/gtSeedThreshold_doublethr.m
index 5382d7b1fbd465ba7065190febda4590eab7cc16..2d5873d619f1d77ef0c79bd9b9da60f664777f69 100644
--- a/2_difspot/gtSeedThreshold_doublethr.m
+++ b/2_difspot/gtSeedThreshold_doublethr.m
@@ -4,31 +4,29 @@ function gtSeedThreshold_doublethr(first, last, workingdirectory)
% --------------------------------------------------------
%
% It finds seeds by thresholding full images individually at the value
-% parameters.seg.thr_seed. Seeds are the single highest pixels in each
+% parameters.seg.thr_seed. Seeds are the single highest pixels in each
% connected region.
%
% Puts the seeds into a database table to be used for double threshold
-% segmention. It also puts the median background value for the full
+% segmention. It also puts the median background value for the full
% images into a database table.
%
% The segmentation script waits for the full median values table to be
-% completed before starting. For this reason complete the table even
+% completed before starting. For this reason complete the table even
% if not subtracting the background, doesn't waste that much effort
%
%
+% Version 002 May-2012 by P.Reischig
+% Update to new parameters names; use of bwconncomp instead of bwlabel for
+% labelling images; cleaning
%
+% Modified by Nicola Vigano', 2012, nicola.vigano@esrf.fr
+% Added EDF header recycling
%
-% Version 002 May-2012 by P.Reischig
-% update to new parameters names; use of bwconncomp instead of bwlabel
-% for labelling images; cleaning
-%
-
-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% setup
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
if isdeployed
first = str2double(first);
last = str2double(last);
@@ -41,7 +39,6 @@ end
fprintf('Changing directory to %s\n',workingdirectory)
cd(workingdirectory)
-
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% load and unpack parameters
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -53,56 +50,52 @@ table_fullmedianvals = sprintf('%sfullmedianvals', parameters.acq.name);
gtDBConnect();
-
+info = [];
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% main loop through images
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
for zz = first:last
-
- [im, med_val] = pfReadAndThreshold(zz, parameters, NaN);
% NaN argument means this returns the greyscale image without thresholding
-
+ [im, med_val, info] = gtReadAndThreshold(zz, parameters, NaN, true, info);
+
% while doing this, fill in the fullmedianvals table
- mym(sprintf('update %s set val=%0.20g where ndx=%d', ...
+ mym(sprintf('UPDATE %s SET val=%0.20g WHERE ndx=%d', ...
table_fullmedianvals, med_val, zz));
-
+
% thr_seed threshold
thr_im = im > parameters.seg.thr_seed;
thr_im = bwmorph(thr_im, 'open');
-
+
% label (2D only)
% bwconncomp gives:
% labels.NumObjects - number of labels
% labels.PixelIdxList{ii} - linear indices in input image for label ii
labels = bwconncomp(thr_im);
-
+
% pick out seeds
list = [];
-
+
for ii = 1:labels.NumObjects
-
% marker size test
if (length(labels.PixelIdxList{ii}) > parameters.seg.seedminarea)
-
+
[graylevel, index] = max(im(labels.PixelIdxList{ii}));
-
+
[yy, xx] = ind2sub(size(im), labels.PixelIdxList{ii}(index));
-
+
list(end+1, 1:5) = [xx yy zz graylevel 0];
% could also add the bounding boxes of the seeds
end
end
-
-
+
% write seeds to database
% seedID x y z value bad
if (size(list, 1) > 0)
- dbInsertMultiple(table_seeds, 'x', list(:,1)', 'y', list(:,2)', ...
- 'z', list(:,3)', 'graylevel', list(:,4)', 'bad', list(:,5)');
+ dbInsertMultiple( table_seeds, ...
+ 'x', list(:,1)', 'y', list(:,2)', 'z', list(:,3)', ...
+ 'graylevel', list(:,4)', 'bad', list(:,5)');
end
-
end % end for
-
end % of main function
diff --git a/2_difspot/gtSegmentDiffractionBlobs.m b/2_difspot/gtSegmentDiffractionBlobs.m
index 5da50294e9b79426a13fece8bed9327a03448814..90e9ecdd0a0f002aa0074c3cb162c7171a841abf 100644
--- a/2_difspot/gtSegmentDiffractionBlobs.m
+++ b/2_difspot/gtSegmentDiffractionBlobs.m
@@ -6,7 +6,7 @@ function gtSegmentDiffractionBlobs(first, last, workingdirectory)
% finds and labels connected regions in three dimensions; writes each blob
% to the database as it finds them to ease database traffic.
%
-% Uses pfReadAndThreshold that can subtract each full image's remaining
+% Uses gtReadAndThreshold that can subtract each full image's remaining
% median background to offset it to zero before segmentation (it is
% calculated and applied outside the seg.bbox area).
%
@@ -80,7 +80,7 @@ disp('THIS DOES NOT WRAP OVER THE END OF THE DATASET PROPERLY!')
% read the size of one image to make an estimate for the number we can read
% at once:
-test = pfReadAndThreshold(first, parameters, NaN);
+test = gtReadAndThreshold(first, parameters, NaN);
details = whos('test');
maxMemoryUsage = 100; % in MB
@@ -112,7 +112,7 @@ for currentfilendx = first:step:last
for n = 1:step
% Read and threshold image with parameters.seg.thr_single
- shortVol(:,:,n) = pfReadAndThreshold(currentfilendx + n - 1, parameters);
+ shortVol(:,:,n) = gtReadAndThreshold(currentfilendx + n - 1, parameters);
% add a median filter to de-noise the thresholded images
% !!! This a second median filter on the full images that
diff --git a/2_difspot/gtSegmentDiffractionBlobs_doublethr.m b/2_difspot/gtSegmentDiffractionBlobs_doublethr.m
index 49ce98d4f8ee7bd23f92aa7dcc7fe70f16258ac3..e1a6901f63884f99f50d0753ff3af630cd109f55 100644
--- a/2_difspot/gtSegmentDiffractionBlobs_doublethr.m
+++ b/2_difspot/gtSegmentDiffractionBlobs_doublethr.m
@@ -418,7 +418,7 @@ if all(bb(3:4) > minblobsize(1:2)) % size test
% from original gtSegmentDiffractionBlobs
mym(dbInsert(table_difblob, 'difblobID', 0))
- difblobID = mym('select last_insert_id()');
+ difblobID = mym('SELECT last_insert_id()');
fprintf('***DB WRITE *** Blob %d:inserting %d rows, grown from seed %d\n\n',...
difblobID, length(xx), seedID)
@@ -565,7 +565,7 @@ for z = bb(3):(bb(3)+bb(6)-1)
% if we don't have the median value we need, calculate it
if background_subtract
if isnan(fullmedianvals(z+1))
- bg = mym(sprintf('select val from %s where ndx=%d', table_fullmedianvals, z));
+ bg = mym(sprintf('SELECT val FROM %s WHERE ndx=%d', table_fullmedianvals, z));
fullmedianvals(z+1) = bg;
else
bg = fullmedianvals(z+1);
@@ -581,27 +581,12 @@ end
% set anything inside the seg bounding box to zeros
% put seg.bbox relative to the volume
% work out which pixels to set to zero
-firstx = segbb(1)-bb(1)+1;
-firsty = segbb(2)-bb(2)+1;
-lastx = firstx+segbb(3)-1;
-lasty = firsty+segbb(4)-1;
-
-% in x
-if firstx < 1
- firstx = 1;
-end
-if lastx > bb(4)
- lastx = bb(4);
-end
-
+[firstx, firsty] = deal(segbb(1) - bb(1) + 1, segbb(2) - bb(2) + 1);
+[lastx, lasty] = deal(firstx + segbb(3) - 1, firsty + segbb(4) - 1);
-% in y
-if firsty < 1
- firsty = 1;
-end
-if lasty > bb(5)
- lasty = bb(5);
-end
+% fix limits
+[firstx, firsty] = max([firstx firsty], 1);
+[lastx, lasty] = min([lastx, lasty], [bb(4), bb(5)]);
if ~(firstx>bb(4) || lastx<1 || firsty>bb(5) || lasty<1)
% if we have to do something about it
diff --git a/2_difspot/gtSetupSegmentation.m b/2_difspot/gtSetupSegmentation.m
index 7cfaacaeed3a7fbae65794433aeb1c5e52d98d56..45dda432a840f33f168762bce24c03a51e0a248d 100644
--- a/2_difspot/gtSetupSegmentation.m
+++ b/2_difspot/gtSetupSegmentation.m
@@ -331,7 +331,7 @@ sfDoThresholding();
sfUpdateParameters();
% remove the median background at this point - copy paste from
- % pfReadAndThreshold
+ % gtReadAndThreshold
tmpim = im.full(:,:,StackIndex);
if isfield(parameters.seg, 'background_subtract') && ...
(parameters.seg.background_subtract==true)
diff --git a/2_difspot/pfReadAndThreshold.m b/2_difspot/pfReadAndThreshold.m
deleted file mode 100644
index edfdb5fe18182c5eaf2a7562f2e30d24289c24ec..0000000000000000000000000000000000000000
--- a/2_difspot/pfReadAndThreshold.m
+++ /dev/null
@@ -1,100 +0,0 @@
-function [im, med_value] = pfReadAndThreshold(ndx, parameters, varargin)
-% PFREADANDTHRESHOLD Reads the full image with number 'ndx' and thresholds
-% it. It can also return the median value of the full image.
-%
-% It sets the image to zero inside the segmentation bounding box
-% (parameters.seg.bbox) and outside where it is under the threshold.
-% Can subtract the remaining median background of the full image
-% (calculated and applied outside seg.bbox).
-% Thresholds to seg.thr_single by default, or allow another threshold
-% value to be passed in. Pass in NaN to return the greyscale image without
-% thresholding.
-%
-%
-% INPUT
-% ndx - full image number to be read
-% parameters.
-% prep.correct_drift
-% prep.correct_drift_iteration
-%
-% seg.thr_single - the threshold value to be applied
-% seg.bbox - bounding box of area omitted in segmentation
-% seg.background_subtract - if true, the full image's median will be
-% offset to zero
-%
-% varargin{1} - threshold value that overrides seg.thr_single;
-% if NaN, no thresholding is done
-% varargin{2} - if true, no text will be displayed
-%
-%
-% OUTPUT
-% im - segmented image
-% med_value - median value of the full image
-%
-%
-% Version 002 08-05-2012 by P.Reischig
-% Updated to new parameters (thr_single) and cleaned.
-%
-%
-%
-
-seg = parameters.seg;
-prep = parameters.prep;
-
-% if a threshold other than th2 is passed in
-if isempty(varargin)
- thr_single = seg.thr_single;
-else
- thr_single = varargin{1};
-end
-
-if length(varargin)==2
- nodisp = varargin{2};
-else
- nodisp = 0;
-end
-
-% should we wait for images to be shifted by gtApplyDrifts?
-waitfortranslated = false;
-if isfield(prep, 'correct_drift') && strcmp(prep.correct_drift, 'required')
- waitfortranslated = prep.correct_drift_iteration;
-end
-
-fname = sprintf('1_preprocessing/full/full%04d.edf',ndx);
-
-if ~nodisp
- disp(sprintf('now processing image %s',fname));
-end
-
-im_full = edf_wait_read(fname, [], waitfortranslated);
-
-% would be very easy to add this as an option in gtCreateFullLive - do
-% it once there and then not again...
-if (isfield(seg, 'background_subtract') && (seg.background_subtract == true))
- %subtract the median of the background
- %taken from gtFullStatCondor - thanks Peter!
- nullbb = NaN(seg.bbox(4), seg.bbox(3));
- imn = gtPlaceSubImage(nullbb, im_full, seg.bbox(1), seg.bbox(2));
- imn = imn(~isnan(imn(:)));
-
- med_value = median(imn);
- im_full = im_full - med_value;
-
- if ~nodisp
- disp('subtracting median background value')
- end
-else
- med_value = NaN;
-end
-
-% now blank out the extinction image in the centre
-im = gtPlaceSubImage(zeros(seg.bbox(4), seg.bbox(3)), ...
- im_full, seg.bbox(1), seg.bbox(2));
-
-
-% do the thresholding
-if ~isnan(thr_single)
- im(im < thr_single) = 0;
-end
-
-end
diff --git a/zUtil_DB/dbInsert.m b/zUtil_DB/dbInsert.m
index 01491ec73dc1f7de0396633b55565702f4ca59b6..339c36f30358ffd78b014d9ba271b510c1891aa3 100644
--- a/zUtil_DB/dbInsert.m
+++ b/zUtil_DB/dbInsert.m
@@ -1,20 +1,19 @@
- function cmd=dbInsert(table,varargin)
- % modified 10/12/2007 to use mantissa/exponent (%g) for double precision
- % modified 13/12/2007 to use mantissa/exponent (%0.20g) for double precision /Peter/
+function cmd = dbInsert(table, varargin)
+% modified 10/12/2007 to use mantissa/exponent (%g) for double precision
+% modified 13/12/2007 to use mantissa/exponent (%0.20g) for double precision /Peter/
+% Modified by Nicola Vigano', 2012, ID11 @ ESRF vigano@esrf.eu
- beginning=sprintf('insert into %s (',table);
- middle1=[];
- for n=1:2:nargin-1
- middle1=[middle1 sprintf('%s,',varargin{n})];
- end
- middle1=[middle1(1:end-1) ') values ('];
- middle2=[];
+ titles = varargin(1:2:end);
+ titles(2, :) = {','};
- for n=2:2:nargin-1
- middle2=[middle2 sprintf('"%0.20g",',varargin{n})];
- end
-
- middle2(end)=')';
-
- cmd=[beginning middle1 middle2];
+ columns = varargin(2:2:end);
+ numColumns = length(columns);
+ rawColumns = cat(1, columns{:});
+ tuplePattern(1, 1:numColumns) = {'%0.20g'};
+ tuplePattern(2, 1:numColumns) = {','};
+ tuplePattern = [tuplePattern{1:end-1}];
+
+ cmd = [ 'INSERT INTO ' table ' (' titles{1:end-1} ') VALUES ' ...
+ '(' sprintf(tuplePattern, rawColumns) ')'];
+end
diff --git a/zUtil_EDF/edf_wait_read.m b/zUtil_EDF/edf_wait_read.m
index a1237b313df351bae5e0dcce7ae08a54a87f0305..c76974cf47577fa50753fd3637255b595fec721e 100644
--- a/zUtil_EDF/edf_wait_read.m
+++ b/zUtil_EDF/edf_wait_read.m
@@ -1,4 +1,4 @@
-function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
+function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated, info)
% EDF_WAIT_READ.M Reads edf if available, otherwise wait 10s and try again...
% Usage:
% data = edf_wait_read(filename[, bb, waitfortranslated]);
@@ -50,7 +50,9 @@ function [img, varargout] = edf_wait_read(fname, bb, waitfortranslated)
translated = false;
while ~translated
try
- info = edf_info(fname);
+ if (~exist('info', 'var'))
+ info = edf_info(fname);
+ end
if isfield(info, 'istranslated') && (str2double(info.istranslated) == waitfortranslated)
translated = true;
%disp('file has been translated!')