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Commit 698e34ba authored by Laura Nervo's avatar Laura Nervo
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gtCopyCorrectUndistortCondor : stripped out the edf_rename sub-function to be a real function. 

Created zUtil_EDF/edf_rename.m

Signed-off-by: default avatarLaura Nervo <laura.nervo@esrf.fr>
parent bf901faf
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1_preprocessing/gtCopyCorrectUndistortCondor.m
+ 0
− 74
View file @ 698e34ba
......@@ -182,79 +182,5 @@ while (~should_stop)
end
end
disp('Timed out while waited for files to appear... quitting')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% sfCopy was a single subfunction in several scripts - I have created a
% single gtCopy function to be used in all cases
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function newname = edf_rename(oldname, parameters)
% GTCOPYCORRECTUNDISTORTCONDOR/SFRENAME Determines how files should be renamed
% Name convention, description of scheme:
%
% for 80 images collected over two turns
% note this would be nproj=40 in ftomosetup, so be careful!
% keep parameters.acq.nproj as images/180degrees in final data
%
% first turn:
% ref0000_0000.edf..., name_0_0000.edf, name_0_0001.edf... name_0_0039.edf,
% ref0000_0040.edf
%
% second turn: (This was probably true in the past)
% name_1_0000.edf, name_1_0001.edf... name_1_0039.edf, ref0000_1_0040.edf
% second turn: (This is TRUE now)
% name_1_0000.edf, name_1_0001.edf... name_1_0039.edf, ref0000_0040_1.edf
[~, fname, ext] = fileparts(oldname);
if (strcmp(ext, '.edf') && ~(strncmpi(fname, 'dark', 4)))
% we want sequentially number filenames and references groups, without
% the turn indication.
if (strncmpi(fname, 'ref', 3) || strncmpi(fname, 'quali', 5))
splitted_name = regexp(fname, '_', 'split');
% bad idea to name scans ref* or quali*!
switch (numel(splitted_name))
case 3
chief_turn = str2double(splitted_name{end});
old_number = str2double(splitted_name{end-1});
case 2
chief_turn = 0;
old_number = str2double(splitted_name{end});
otherwise
% don't rename / renumber / overwrite if not sure!
gtError('gtCopyCorrectUndistortCondor:wrong_renaming', ...
'dont recognise the name of this edf!')
end
% keep the ref00xx_ and quali_ part of the name
base_name = [splitted_name{1} '_'];
elseif (strncmpi(fname, parameters.acq.name, length(parameters.acq.name)))
% We remove the assumption of '_' at the end of the acquisition name
numbers_name = strrep(fname, parameters.acq.name, '');
splitted_name = regexp(numbers_name, '_', 'split');
% if this is an image.
if (parameters.acq.interlaced_turns > 0)
chief_turn = str2double(splitted_name{end-1});
else
chief_turn = 0;
end
old_number = str2double(splitted_name{end});
base_name = parameters.acq.name;
else
% don't rename / renumber / overwrite if not sure!
gtError('gtCopyCorrectUndistortCondor:wrong_renaming', ...
'dont recognise the name of this edf!')
end
images_per_turn = (2 * parameters.acq.nproj) ...
/ (parameters.acq.interlaced_turns + 1);
new_number = old_number + (chief_turn * images_per_turn);
% note that in some datasets we exceed 9999 images.
newname = sprintf('%s%04d.edf', base_name, new_number);
else
% Either not an edf file or darks
newname = oldname;
end
end
zUtil_EDF/edf_rename.m 0 → 100644
+ 67
− 0
View file @ 698e34ba
function newname = edf_rename(oldname, parameters)
% EDF_RENAME Determines how files should be renamed
% Name convention, description of scheme:
%
% for 80 images collected over two turns
% note this would be nproj=40 in ftomosetup, so be careful!
% keep parameters.acq.nproj as images/180degrees in final data
%
% first turn:
% ref0000_0000.edf..., name_0_0000.edf, name_0_0001.edf... name_0_0039.edf,
% ref0000_0040.edf
%
% second turn: (This was probably true in the past)
% name_1_0000.edf, name_1_0001.edf... name_1_0039.edf, ref0000_1_0040.edf
% second turn: (This is TRUE now)
% name_1_0000.edf, name_1_0001.edf... name_1_0039.edf, ref0000_0040_1.edf
[~, fname, ext] = fileparts(oldname);
if (strcmp(ext, '.edf') && ~(strncmpi(fname, 'dark', 4)))
% we want sequentially number filenames and references groups, without
% the turn indication.
if (strncmpi(fname, 'ref', 3) || strncmpi(fname, 'quali', 5))
splitted_name = regexp(fname, '_', 'split');
% bad idea to name scans ref* or quali*!
switch (numel(splitted_name))
case 3
chief_turn = str2double(splitted_name{end});
old_number = str2double(splitted_name{end-1});
case 2
chief_turn = 0;
old_number = str2double(splitted_name{end});
otherwise
% don't rename / renumber / overwrite if not sure!
gtError('gtCopyCorrectUndistortCondor:wrong_renaming', ...
'dont recognise the name of this edf!')
end
% keep the ref00xx_ and quali_ part of the name
base_name = [splitted_name{1} '_'];
elseif (strncmpi(fname, parameters.acq.name, length(parameters.acq.name)))
% We remove the assumption of '_' at the end of the acquisition name
numbers_name = strrep(fname, parameters.acq.name, '');
splitted_name = regexp(numbers_name, '_', 'split');
% if this is an image.
if (parameters.acq.interlaced_turns > 0)
chief_turn = str2double(splitted_name{end-1});
else
chief_turn = 0;
end
old_number = str2double(splitted_name{end});
base_name = parameters.acq.name;
else
% don't rename / renumber / overwrite if not sure!
gtError('gtCopyCorrectUndistortCondor:wrong_renaming', ...
'dont recognise the name of this edf!')
end
images_per_turn = (2 * parameters.acq.nproj) ...
/ (parameters.acq.interlaced_turns + 1);
new_number = old_number + (chief_turn * images_per_turn);
% note that in some datasets we exceed 9999 images.
newname = sprintf('%s%04d.edf', base_name, new_number);
else
% Either not an edf file or darks
newname = oldname;
end
end
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