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Update load_imgs
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+ Better read NRC images.
+ Better comments.
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@tsipkens
tsipkens committed Jan 20, 2024
1 parent 7d9c8f3 commit 10cbc9e
Showing 1 changed file with 67 additions and 64 deletions.
131 changes: 67 additions & 64 deletions +tools/load_imgs.m
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Original file line number Diff line number Diff line change
Expand Up @@ -161,14 +161,14 @@

footer_found = 0; % flag whether footer was found

f_nm = 1; % flag indicating nanometers (detected below)
fl_nm = 1; % flag indicating nanometers (detected below)

% Search for row satisying
f_footrow = sum(Imgs(jj).raw, 2) > ...
(0.9 * size(Imgs(jj).raw, 2) * white);
ii = find(f_footrow, 1); % first 90% white row

% If failed, instead look for black.
% If failed, instead look for black (e.g., NRC footer).
if isempty(ii)
f_footrow = sum(Imgs(jj).raw, 2) == 0;
ii = find(f_footrow, 1); % first black row
Expand All @@ -182,59 +182,62 @@

%-- Detecting magnification and/or pixel size ----------------%
if license('test', 'video_and_image_blockset') % check if toolbox for OCR is installed
o1 = ocr(footer);

%-- OCR ------------------------------------------------------%
o1 = ocr(footer); % first try, straight OCR on footer

% If failed, try again on binary image.
if isempty(o1.Text)
o1 = ocr(footer > 0);
end

Imgs(jj).ocr = o1;
% If text not as expected. Retry OCR. This time without scale bar.
if ~any(contains(o1.Text, {'nm', 'pm', 'um'}))
rp = regionprops(footer > 0);
ar = [rp.BoundingBox];
ar = reshape(ar', [4, length(ar)/4])';
ar = ar(:,3) ./ ar(:,4); % arrive at aspect ratio
[~, ar_max] = max(ar);
rp_bb = floor(rp(ar_max).BoundingBox);

% Look for pixel size.
footer_nobar = footer;
footer_nobar(rp_bb(2):rp_bb(2)+rp_bb(4), ...
rp_bb(1):rp_bb(1)+rp_bb(3)) = 0; % remover scale bar before OCR

o1 = ocr(footer_nobar > 0);
end

Imgs(jj).ocr = o1;

%-- Interpret OCR text ---------------------------------------%
% Look for pixel size directly.
txts = {'nm/pix', 'nmlpix', 'nm/plx', 'nm/101x',...
'um/pix', 'umlpix','um/plx', 'um/101x',...
'pm/pix', 'pmlpix','pm/plx', 'pm/101x', ...
'nm', 'um'};
'nm', 'um', 'pm'};

% Loop through options. Flag if nm/um.
for kk = 1:length(txts)
pixsize_end = strfind(o1.Text, txts(kk)) - 1;
if ~isempty(pixsize_end)
% Mark if unit read is not nm.
if or(contains(txts(kk), 'um'), ...
contains(txts(kk), 'pm'))
f_nm = 0;
fl_nm = 0;
end
break;
end
end

% Alternative footer at NRC (black footer with scale bar).
% Scale bar code from below.
if isempty(pixsize_end)
footer = footer > 0;
rp = regionprops(footer);
ar = [rp.BoundingBox];
ar = reshape(ar', [4, length(ar)/4])';
ar = ar(:,3) ./ ar(:,4); % arrive at aspect ratio
[~, ar_max] = max(ar); len = rp(ar_max).BoundingBox(3); % pixel length of scale bar

o2 = split(o1.Text); o2 = str2num(o2{1});
if or(contains(o1.Text, 'pm'), contains(o1.Text, 'um'))
o2 = o2 .* 1000;
end

Imgs(jj).pixsize = o2 / len;
tools.textbar([jj, length(Imgs)]);
continue;
end

%-- Interpret OCR text and compute pixel size --------------------%
%-- Interpret scale/number in footer -------------------------%
txts2 = {'Cal:', 'cal:', 'Ca1:', 'ca1:', 'CaI:', 'caI:',...
'Cal-', 'cal-', 'Ca1-', 'ca1-', 'CaI-', 'caI-',...
'Cal''', 'cal''', 'Ca1''', 'ca1''', 'CaI''', 'caI''',...
'Cal"', 'cal"', 'Ca1"', 'ca1"', 'CaI"', 'caI"',...
'Cal ', 'cal ', 'Ca1 ', 'ca1 ', 'CaI ', 'caI ',};

% Check if one can find any of the above strings.
% Then a per pixel value is reported directly.
for kk = 1:length(txts2)
pixsize_start = strfind(o1.Text, txts2(kk)) + 5;
if ~isempty(pixsize_start)
Expand All @@ -246,7 +249,9 @@
% determine if one can find appropriate range.
if isempty(pixsize_start)
pixpick = pixsize_end - 2; % initialize two before end
while isempty(pixsize_start)
if pixpick < 3; pixsize_start = 1; end % then just select all text and continue

while and(isempty(pixsize_start), pixpick > 0)
if isnan(str2double(o1.Text(pixpick))) &&...
(o1.Text(pixpick - 2) == ' ') ||...
(o1.Text(pixpick - 2) == newline) % search for newline or space
Expand All @@ -257,48 +262,46 @@
end
end

% Save relevant text to variable.
o1_num = o1.Text(pixsize_start:pixsize_end);

% Check if numbers where misrepresented by characters
% e.g., zero was misread as "O"
o1_Text = o1.Text(pixsize_start:pixsize_end);
if isnan(str2double(o1_Text))
o1_Text = strrep(o1_Text, 'o', '0');
o1_Text = strrep(o1_Text, 'O', '0');
o1_Text = strrep(o1_Text, '‘', '');

I_chk = strfind(o1_Text, 'I');
if any(I_chk == 2)
o1_Text(I_chk(I_chk == 2)) =...
strrep(o1_Text(I(I_chk == 2)), 'I', '.');
end
o1_Text = strrep(o1_Text, 'I', '1');

l_chk = strfind(o1_Text, 'l');
if any(l_chk == 2)
o1_Text(l_chk(l_chk == 2)) =...
strrep(o1_Text(l(l_chk == 2)), 'l', '.');
end
o1_Text = strrep(o1_Text, 'l', '1');

T_chk = strfind(o1_Text, 'T');
if any(T_chk == 2)
o1_Text(T_chk(T_chk == 2)) =...
strrep(o1_Text(T(T_chk == 2)), 'T', '.');
end
o1_Text = strrep(o1_Text, 'T', '1');
if isnan(str2double(o1_num))
o1_num = strrep(o1_num, 'o', '0');
o1_num = strrep(o1_num, 'O', '0');
o1_num = strrep(o1_num, '‘', '');

o1_num = strrep(o1_num, 'I', '1');
o1_num = strrep(o1_num, 'l', '1');

spc_chk = strfind(o1_Text, ' ');
if any(spc_chk == 2)
o1_Text(spc_chk(spc_chk == 2)) =...
strrep(o1_Text(spc_chk(spc_chk == 2)), ' ', '.');
end
o1_Text = strrep(o1_Text, ' ', '');
o1_num = strrep(o1_num, 'T', '1');
o1_num = strrep(o1_num, ' ', '');
end

% Convert to a number.
o1_num = str2double(o1_num);

% If not /px value, then need to interpret scale bar.
% Scale bar code from below.
% Alternative footer at NRC (black footer with scale bar).
if ~any(contains(o1.Text, {'pix', 'px', 'plx', '101x', 'Ca'}))
footer = footer > 0;
rp = regionprops(footer);
ar = [rp.BoundingBox];
ar = reshape(ar', [4, length(ar)/4])';
ar = ar(:,3) ./ ar(:,4); % arrive at aspect ratio
[~, ar_max] = max(ar);
len = rp(ar_max).BoundingBox(3); % pixel length of scale bar

o1_num = o1_num / len;
end

% Finally, convert formatted text to a number.
Imgs(jj).pixsize = str2double(o1_Text);
Imgs(jj).pixsize = o1_num;

% Convert pixsize to nm.
if f_nm == 0 % if given in micrometers
if fl_nm == 0 % if given in micrometers
Imgs(jj).pixsize = Imgs(jj).pixsize * 1e3;
end

Expand Down Expand Up @@ -361,7 +364,7 @@
Imgs(jj).pixsize = sc_length / len;

% If given in micrometers, convert.
if f_nm==0; Imgs(jj).pixsize = Imgs(jj).pixsize * 1e3; end
if fl_nm==0; Imgs(jj).pixsize = Imgs(jj).pixsize * 1e3; end


% NOTE: Show bw1 image to see the binary that should include
Expand Down

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