-
Notifications
You must be signed in to change notification settings - Fork 2
/
PatchChart.cpp
417 lines (381 loc) · 16.2 KB
/
PatchChart.cpp
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
#define _CRT_SECURE_NO_WARNINGS
/*
Copyright (c) <2020> <doug gray>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
#include "PatchChart.h"
#pragma warning (disable : 4018 )
using std::vector;
using std::string;
using std::pair;
using std::array;
// Read RGB from tif file into a 2D Array
Array2D<V3> FromTiffReader(string arg)
{
ArrayRGB rgb = TiffRead(arg.c_str(), 1.0);
Array2D<V3> rgbout(rgb.nr, rgb.nc);
for (int i = 0; i < rgb.nr; i++)
for (int ii = 0; ii < rgb.nc; ii++)
{
rgbout(i, ii)[0] = rgb(i, ii, 0);
rgbout(i, ii)[1] = rgb(i, ii, 1);
rgbout(i, ii)[2] = rgb(i, ii, 2);
}
return rgbout;
}
/// <summary>
/// Get minimum of r, g, or b in an rgb array as gray scale array
/// </summary>
/// <param name="rgbin"></param>
/// <returns></returns>
Array2D<float> get_min_rgb(const Array2D<V3>& rgbin)
{
Array2D<float> rgbout(rgbin.nr, rgbin.nc);
for (int i = 0; i < rgbin.nr; i++)
for (int ii = 0; ii < rgbin.nc; ii++)
{
rgbout(i, ii) = static_cast<float>(std::min({ rgbin(i,ii)[0], rgbin(i,ii)[1], rgbin(i,ii)[2] }));
}
return rgbout;
}
float get_tilt(const Array2D<float>& v, int offset)
{
return 0;
}
struct AveStd { float ave, std; };
int get_boundary(const vector<AveStd>& v, float min, float max)
{
for (int i = int(v.size()) / 3; i > 0; i--)
{
// allow for 15% reduction from max white value for white border detection
if (v[i].ave > .85 * max && v[i].std < .05)
{
for (int ii = 0; ii < 20; ii++)
if (v[i + ii].ave < (v[i].ave + v[i + 20].ave) / 2.0f)
return i + ii;
}
}
return 1;
};
/// <summary>
/// Get top and bottom boundary of patches
/// </summary>
/// <param name="v"></param>
/// <returns></returns>
pair<int,int> strips_info(const Array2D<float>& v) {
auto minmax = std::minmax_element(v.v.begin(), v.v.end());
vector<AveStd> strips(v.nr);
for (int i = 0; i < v.nr; i++)
{
Statistics strip;
for (int ii = 0; ii < v.nc; ii++) // copy a row
strip.clk(v(i, ii));
strips[i].ave = strip.ave();
strips[i].std = strip.std();
}
int top = get_boundary(strips, *minmax.first, *minmax.second);
std::reverse(strips.begin(), strips.end());
int bottom = int(strips.size()) - get_boundary(strips, *minmax.first, *minmax.second);
return std::pair<int, int>(top, bottom);
};
/// <summary>
/// return top and bottom of image assuming white border
/// </summary>
/// <param name="g_in"></param>
/// <param name="flip"></param> if true, rotate image 90 degrees clockwise
/// <returns></returns>
pair<size_t, size_t> get_patch_ends(const Array2D<float>& g_in, bool flip)
{
auto g = flip ? transpose(g_in) : g_in;
//TiffWrite("test\\test_image.tif", g);
return strips_info(g);
}
/// <summary>
/// get ave and std for each set of pixels at fixed distances from patch edges
/// </summary>
/// <param name="sorted_pixels"></param> sorted by descending distance from edge
/// <returns></returns>
vector<std::pair<V3, V3>> get_dist_means(vector<BlockVal> const &sorted_pixels)
{
vector<std::pair<V3,V3>> ret(sorted_pixels[0].dist+1);
int high = sorted_pixels[0].dist;
int low = sorted_pixels[sorted_pixels.size()-1].dist;
validate(high > 5, "too few pixels in patch, must be > 5 from center");
validate(low ==0, "center must be '0' dist");
auto start = sorted_pixels.begin();
for (int i = high; i >= 0; i--)
{
RGB_Stat stat;
while (start != sorted_pixels.end() && start->dist == i)
{
stat.clk(start->pixel);
start++;
}
ret[i].first = stat.ave();
ret[i].second = stat.std();
}
return ret;
}
// get statistics from a patch of pixels discarding outliers
/// <summary>
/// PatchStats::rgb has best average value of inner patch pixels
/// </summary>
/// <param name="sample"> vector containing pixel and distance from nearest edge
/// sorted starting from center pixels to edge pixels</param>
/// <returns></returns>
PatchStats process_sample(const vector<BlockVal>& sample)
{
const float thresh_ctr = .3f; // thresh_ctr of pixels that are closest to center
const float thresh_std = .7f; // thresh_std of lowest errs from the mean to discard lint/fiber reflections
PatchStats ret;
//ret.aves = get_dist_means(sample);
RGB_Stat stats;
RGB_Stat dist1;
size_t breakpoint = int(round(thresh_ctr*sample.size()));
while (sample[breakpoint].dist == sample[breakpoint + 1].dist)
breakpoint++; // forward to next dist increment
vector<pair<V3, float>> rgb_set(breakpoint);
for (size_t i = 0; i < breakpoint; i++)
stats.clk(sample[i].pixel);
V3 ave = stats.ave();
for (size_t i = 0; i < breakpoint; i++)
rgb_set[i] = pair<V3, float>{ sample[i].pixel, dist(sample[i].pixel, ave)};
// sort based on error from mean then remove the largest 1/3
sort(rgb_set.begin(), rgb_set.end(), [](const pair<V3, float>& a, const pair<V3, float>& b) {return a.second < b.second; });
rgb_set.resize(int(round(rgb_set.size()*thresh_std)));
RGB_Stat final;
for (auto& x : rgb_set)
final.clk(x.first);
ret.rgb = final.ave();
ret.rgb_err = final.std();
// look at variation in deciles from closest to center to edges
int steps = int(sample.size() / ret.errs.size());
for (int i = 0; i < ret.errs.size(); i++)
{
RGB_Stat stat;
for (int ii = i * steps; ii < (i + 1) * steps; ii++)
stat.clk(sample[ii].pixel);
ret.errs[i] = dist(stat.std());
}
return ret;
}
// get statistics over the entire set of patches column by column
vector<vector<PatchStats>> process_samples(const vector<vector<vector<BlockVal>>>& samples)
{
vector<vector<PatchStats>> ret;
for (auto& x : samples) {
vector<PatchStats> columns;
for (auto& xx : x)
{
columns.push_back(process_sample(xx));
}
ret.push_back(columns);
}
return ret;
}
// return metrics for patches sizes from arg:start to maxRowsAndCols
// smallest metric indicates number of patches in row or column
vector<double> find_patch_metric(vector<double>& v, int start)
{
vector<double> change(maxRowsAndCols+1);
for (int cnt = start; cnt < change.size(); cnt++)
{
double delta = 1.0 * v.size() / cnt;
double delta5 = round(.2 * delta);
double largest = 0;
auto skip = [&v, delta, delta5](int i, int id5) {
auto x = static_cast<int>(std::round(i * delta + id5 * delta5));
if (x >= v.size())
x = static_cast<int>(v.size() - 1);
return x;
};
for (int i = 0; i < cnt; i++)
{
auto t1 = std::accumulate(v.begin() + skip(i, 1), v.begin() + skip(i, 2), 0.);
auto t2 = std::accumulate(v.begin() + skip(i, 2), v.begin() + skip(i, 3), 0.);
auto t3 = std::accumulate(v.begin() + skip(i, 3), v.begin() + skip(i, 4), 0.);
largest += std::max({ abs(t1 - t2),abs(t2 - t3) }) / delta5;
}
change[cnt] = largest;
}
return change;
}
// get row and col counts using minimums from find_patch_metric
VectorLocs get_rows_and_columns(const Array2D<V3>& rgb, VectorLocs hs, VectorLocs vs)
{
VectorLocs ret;
vector<double> cols(maxRowsAndCols+1);
vector<double> rows(maxRowsAndCols+1);
for (float pass = .005f; pass < .9975f; pass+=.005f) // scan 200 slices and accumulate patch location info
{
vector<double> green_slice_h;
for (size_t i = hs.first; i < hs.second; i++)
green_slice_h.push_back(rgb[int(vs.first + pass*(vs.second-vs.first))] [i] [1]);
vector<double> cols_1 = find_patch_metric(green_slice_h, minRowsAndCols);
for (size_t i = 0; i < cols_1.size(); i++)
cols[i] += cols_1[i];
vector<double> green_slice_v;
for (size_t i = vs.first; i < vs.second; i++)
green_slice_v.push_back(rgb[int(i)][int(hs.first + pass*(hs.second-hs.first))][1]);
vector<double> rows_1 = find_patch_metric(green_slice_v, minRowsAndCols);
for (int i = 0; i < rows_1.size(); i++)
rows[i] += rows_1[i];
}
ret.first = std::min_element(rows.begin() + minRowsAndCols, rows.end()) - rows.begin();
ret.second = std::min_element(cols.begin() + minRowsAndCols, cols.end()) - cols.begin();
return ret;
}
Array2D<V3> refine_image(const Array2D<V3> &rgbin, const Array2D<float> rgbmin, const VectorLocs vs, const VectorLocs hs)
{
auto rgb = rgbin;
// if not enough white space to align assume proper registration
if (vs.first < 10 || hs.first < 10 || rgbmin.nr-vs.second < 10 || rgbmin.nc - hs.second < 10)
return rgb;
auto spread = int(std::max(vs.second - vs.first, hs.second - hs.first)+1);
vector<vector<int>> skew(19, vector<int>(spread));
for (int angle_i = -9; angle_i <= 9; angle_i++)
for (int i = 0; i < spread; i++)
skew[angle_i+9][i] = int(std::round(angle_i * (float(spread/2-i) / (spread/2))));
array<array<float, 19>, 19> s{};
auto first_v = (spread / 2) - (hs.second - hs.first) / 2;
auto first_h = (spread / 2) - (vs.second - vs.first) / 2;
for (int angle_i = -9; angle_i <= 9; angle_i++)
for (int offset = -9; offset <= 9; offset++)
{
Statistics variation;
for (size_t i = hs.first; i < hs.second; i++)
{
variation.clk(rgbmin(int(offset + vs.first + skew[angle_i + 9][i - hs.first+first_v]), int(i - hs.first)));
}
s[angle_i + 9][offset + 9] = variation.std();
}
// min at s[15] for .5 degree tilt CCW
array<float, 19> errsum;
for (int i = 0; i < 19; i++)
errsum[i] = std::accumulate(s[i].begin(), s[i].begin() + 9, 0.0f);
auto angle_fit = std::min_element(errsum.begin(), errsum.end()) - errsum.begin();
std::fill(rgb.v.begin(), rgb.v.end(), V3{ 1.0f,1.0f, 1.0f });
for (int row=int(vs.first); row < int(vs.second); row++)
for (int col = int(hs.first); col < int(hs.second); col++)
{
rgb(row, col) = rgbin(row+skew[angle_fit][col-hs.first+first_v],
col+skew[18-angle_fit][row-vs.first+first_h]);
}
//TiffWrite("test\\testx.tif", rgb,"");
return rgb;
}
// calculate row and col counts then extract data into a 2D grid of patch info
vector<vector<PatchStats>> extract_patch_data(const Array2D<V3>& rgbin)
{
Array2D<float> rgbmin = get_min_rgb(rgbin);
auto vs = get_patch_ends(rgbmin,false); // locate top,bottom of patch grid
validate(vs.first > 0 && vs.second > 0, "No White Space at Top or Bottom detected.");
auto rgbmin1 = rgbmin.clip(Array2D<float>::Extants{ int(vs.first), int(vs.second), 0, int(rgbmin.nc-1) });
auto hs = get_patch_ends(rgbmin1,true); // locate left,right of patch grid
validate(hs.first > 0 && hs.second > 0, "No White Space at Left or Right detected.");
const auto rgb = refine_image(rgbin, rgbmin, vs, hs); // align image so top is parallel
auto [rows, cols] = get_rows_and_columns(rgb, hs, vs);
float hdelta = static_cast<float>(hs.second - hs.first + 1) / cols;
float vdelta = static_cast<float>(vs.second - vs.first + 1) / rows;
vector<vector<vector<BlockVal>>> samples;
for (size_t row = 0; row < rows; row++)
{
vector<vector<BlockVal>> row_samples;
for (size_t col = 0; col < cols; col++)
{
size_t pos_00 = static_cast<size_t>(round(hs.first + hdelta * col));
size_t pos_01 = static_cast<size_t>(round(hs.first + hdelta * (col + 1) - 1));
size_t pos_10 = static_cast<size_t>(round(vs.first + vdelta * row));
size_t pos_11 = static_cast<size_t>(round(vs.first + vdelta * (row + 1) - 1));
vector<BlockVal> patch; patch.reserve((pos_01-pos_00 + 1)*(pos_11 - pos_10 + 1));
//std::cout << pos_00 << " " << pos_01 << " " << pos_10 << " " << pos_11 << "\n";
for (size_t i = pos_00; i < pos_01; i++) // horizontal, second coord
for (size_t ii = pos_10; ii < pos_11; ii++) // vertical, first coord
{
BlockVal spot;
spot.pixel = rgb(static_cast<int>(ii), static_cast<int>(i));
spot.dist = static_cast<int>(std::min({ i - pos_00, ii - pos_10, pos_01 - i - 1, pos_11 - ii - 1 }));
patch.push_back(spot);
}
std::sort(patch.begin(), patch.end(), [](BlockVal& a, BlockVal& b) {return a.dist > b.dist; });
row_samples.push_back(patch);
}
samples.push_back(row_samples);
}
return process_samples(samples);
}
// Extract and add tif image data into charts
bool PatchCharts::init(string tiff_filename, bool landscape)
{
auto scale = [](V3 x_in, float factor) {return V3{ x_in[0] * factor, x_in[1] * factor, x_in[2] * factor }; };
PatchChart chart;
try
{
{
ArrayRGB rgb = TiffRead(tiff_filename.c_str(), 1.0);
if (landscape) // transpose if landscape, Image top must be on left side
{
ArrayRGB rgb1 = rgb;
std::swap(rgb1.nc, rgb1.nr);
for (int color = 0; color < 3; color++)
for (int i = 0; i < rgb.nr; i++)
for (int ii = 0; ii < rgb.nc; ii++)
rgb1(ii, rgb.nr-i-1, color) = rgb(i, ii, color); // Image top must be on left side!
chart.tiff_rgb = rgb1;
}
else
chart.tiff_rgb = rgb;
}
//TiffWrite("x.tif", tmp.tiff_rgb,"");
validate(chart.tiff_rgb.nc > 0, "Invalid image patch file");
if (chart.tiff_rgb.dpi !=200)
chart.tiff_rgb = arrayRGBChangeDPI(chart.tiff_rgb, 200);
chart.rgb = Array2D<V3>(chart.tiff_rgb.nr, chart.tiff_rgb.nc);
for (int i = 0; i < chart.tiff_rgb.nr; i++)
for (int ii = 0; ii < chart.tiff_rgb.nc; ii++)
{
chart.rgb(i, ii)[0] = chart.tiff_rgb(i, ii, 0);
chart.rgb(i, ii)[1] = chart.tiff_rgb(i, ii, 1);
chart.rgb(i, ii)[2] = chart.tiff_rgb(i, ii, 2);
}
chart.patch_data = extract_patch_data(chart.rgb);
chart.rows = static_cast<int>(chart.patch_data.size());
chart.cols = static_cast<int>(chart.patch_data[0].size());
for (size_t i = 0; i < chart.cols; i++)
for (size_t ii = 0; ii < chart.rows; ii++)
{
// scale for 8 bit representation [0-255]
rgb255.push_back(scale(chart.patch_data[ii][i].rgb,255.0f));
rgb_std_255.push_back(scale(chart.patch_data[ii][i].rgb_err,255.0f));
}
}
catch (const char* e) {
err_info = e;
}
charts.push_back(chart);
return true;
}
// Add LAB data to associated RGB data for use in generating ICC profiles
void PatchCharts::add_lab_to_rgb(const vector<V3> & lab)
{
validate(rgb255.size() == lab.size(), "Patch count doesn't match measurement patch count");
for (int i = 0; i < rgb255.size(); i++)
{
validate(!(lab[i][0] > 85 && rgb255[i][1] < 127), "Patches not matching high L* values");
rgblab.push_back(V6{rgb255[i][0], rgb255[i][1], rgb255[i][2], lab[i][0], lab[i][1], lab[i][2] });
}
}