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basisunusbasisunus
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fixed using clipping box to crop volume and save
1 parent 252ac8c commit 28a4105

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12 files changed

+164
-148
lines changed

12 files changed

+164
-148
lines changed

‎FluoRender/FluoRender/Calculate/VolumeSampler.cpp‎

Lines changed: 22 additions & 104 deletions
Original file line numberDiff line numberDiff line change
@@ -46,6 +46,7 @@ VolumeSampler::VolumeSampler() :
4646
m_neg_mask(false),
4747
m_crop_origin(0.0),
4848
m_crop_size(0.0),
49+
m_use_clipbox(false),
4950
m_filter(0),
5051
m_filter_size(0.0),
5152
m_border(0)
@@ -101,9 +102,14 @@ void VolumeSampler::SetNegMask(bool bval)
101102
m_neg_mask = bval;
102103
}
103104

104-
void VolumeSampler::SetClipRotation(const fluo::Quaternion &q)
105+
void VolumeSampler::SetUseClipbox(bool bval)
105106
{
106-
m_q_cl = q;
107+
m_use_clipbox = bval;
108+
}
109+
110+
void VolumeSampler::SetRotation(const fluo::Quaternion &q)
111+
{
112+
m_q = q;
107113
}
108114

109115
void VolumeSampler::SetCenter(const fluo::Point &p)
@@ -162,7 +168,13 @@ void VolumeSampler::Resize(SampDataType type, bool replace)
162168
if (m_size_out.any_le_zero() || m_fix_size)
163169
m_size_out = m_size_in;
164170
//check rotation & translation
165-
bool rot = !m_q_cl.IsIdentity();
171+
auto& cb = input->GetClippingBox();
172+
fluo::Quaternion q_rot;
173+
if (m_use_clipbox)
174+
q_rot = cb.GetRotation();
175+
else
176+
q_rot = m_q;
177+
bool rot = !q_rot.IsIdentity();
166178
bool trans = m_trans != fluo::Vector();
167179
fluo::Vector size = m_size_out - fluo::Vector(0.5);
168180
fluo::Vector size_in = m_size_in - fluo::Vector(0.5);
@@ -175,15 +187,16 @@ void VolumeSampler::Resize(SampDataType type, bool replace)
175187
if (!m_fix_size && rot &&
176188
m_size_out.all_non_zero())
177189
{
178-
rotate_scale(size_in, spc_in, size, spc);
179-
m_size_out = size + fluo::Vector(0.5);
190+
size = cb.GetPlaneSizeIndex();
191+
m_size_out = size;
180192
m_size_out.normalize_at_least_one();
193+
size -= fluo::Vector(0.5);
194+
spc = cb.GetPlaneSizeWorld() / cb.GetPlaneSizeIndex();
181195
}
182196

183197
//recalculate range
184-
auto& cb = input->GetClippingBox();
185-
m_crop_origin = cb.GetBBoxIndex().Min();
186-
m_crop_size = cb.GetBBoxIndex().diagonal();
198+
m_crop_origin = cb.GetClipsUnit().Min() * m_size_out;
199+
m_crop_size = cb.GetClipSizeIndex();
187200
}
188201
else
189202
{
@@ -197,7 +210,6 @@ void VolumeSampler::Resize(SampDataType type, bool replace)
197210
ncenter = fluo::Vector(0.5);
198211
else
199212
ncenter = fluo::Vector(m_center) / m_size_out;
200-
fluo::Quaternion q_cl = m_q_cl;
201213
bool neg = m_neg_mask && (type == SDT_Mask || type == SDT_Label);
202214
if (neg)
203215
{
@@ -246,7 +258,7 @@ void VolumeSampler::Resize(SampDataType type, bool replace)
246258
vec -= ncenter;//center
247259
vec *= spcsize;//scale
248260
fluo::Quaternion qvec(vec);
249-
qvec = (-q_cl) * qvec * (q_cl);//rotate
261+
qvec = (-q_rot) * qvec * (q_rot);//rotate
250262
vec = qvec.GetVector();
251263
vec /= spcsize_in;//normalize
252264
vec += ncenter;//translate
@@ -493,100 +505,6 @@ std::pair<fluo::Point, fluo::Vector> VolumeSampler::xyz2ijkt(const fluo::Point&
493505
return { ijk, t };
494506
}
495507

496-
int VolumeSampler::rotate_scale(fluo::Vector &vsize_in, fluo::Vector &vspc_in,
497-
fluo::Vector &vsize, fluo::Vector &vspc)
498-
{
499-
fluo::Vector rsf = vsize / vsize_in;//rescale factor
500-
std::vector<fluo::Quaternion> qs;
501-
std::vector<fluo::Vector> vs;
502-
std::vector<fluo::Vector> vs2;
503-
qs.push_back(fluo::Quaternion(1, 0, 0, 0));
504-
qs.push_back(fluo::Quaternion(0, 1, 0, 0));
505-
qs.push_back(fluo::Quaternion(0, 0, 1, 0));
506-
fluo::Vector vec_in = vsize_in * vspc_in;
507-
for (auto &q : qs)
508-
{
509-
q = (-m_q_cl) * q * (m_q_cl);
510-
vs.push_back(q.GetVector() * vec_in);
511-
vs2.push_back(q.GetVector() * vspc_in);
512-
}
513-
fluo::Vector rv;
514-
int i = 0;
515-
for (auto &v : vs)
516-
if (i < 3) rv[i++] = v.length();
517-
i = 0;
518-
for (auto &v : vs2)
519-
if (i < 3) vspc[i++] = v.length();
520-
if (vspc.x() == 0.0 ||
521-
vspc.y() == 0.0 ||
522-
vspc.z() == 0.0)
523-
return 0;//invalid
524-
//rescale spcs to maintain sample size
525-
consv_volume(vspc, vspc_in);
526-
if (m_crop)
527-
{
528-
vspc /= rsf;
529-
vsize = rv / vspc;
530-
}
531-
else
532-
{
533-
vsize = rv * rsf / vspc;
534-
}
535-
return 1;
536-
}
537-
538-
int VolumeSampler::consv_volume(fluo::Vector &vec, fluo::Vector &vec_in)
539-
{
540-
double vol = vec.volume();
541-
double vol_in = vec_in.volume();
542-
if (vol == 0.0 || vol_in == 0.0)
543-
return 0;
544-
//conserve volume
545-
if (std::abs(vol - vol_in) >
546-
fluo::Epsilon(3) * vec_in[vec_in.max()])
547-
{
548-
//diff array
549-
double dif[9] = {
550-
vec[0] - vec_in[0], vec[0] - vec_in[1], vec[0] - vec_in[2],
551-
vec[1] - vec_in[0], vec[1] - vec_in[1], vec[1] - vec_in[2],
552-
vec[2] - vec_in[0], vec[2] - vec_in[1], vec[2] - vec_in[2] };
553-
int ind_min;
554-
double val_min, val;
555-
for (int i = 0; i < 9; ++i)
556-
{
557-
val = std::abs(dif[i]);
558-
if (i == 0)
559-
{
560-
val_min = val;
561-
ind_min = i;
562-
}
563-
else
564-
{
565-
if (val < val_min)
566-
{
567-
val_min = val;
568-
ind_min = i;
569-
}
570-
}
571-
}
572-
int ind = ind_min / 3;
573-
int ind_in = ind_min % 3;
574-
//align min dif
575-
double f = std::sqrt(vol_in*vec[ind]/vol/vec_in[ind_in]);
576-
vec[ind] = vec_in[ind_in];
577-
//the remaining 2
578-
for (int i = 0; i < 3; ++i)
579-
{
580-
if (i == ind)
581-
continue;
582-
vec[i] *= f;
583-
}
584-
585-
return 1;
586-
}
587-
return 0;
588-
}
589-
590508
double VolumeSampler::SampleNearestNeighbor(const fluo::Point& coord)
591509
{
592510
auto ijk = xyz2ijk(coord);

‎FluoRender/FluoRender/Calculate/VolumeSampler.h‎

Lines changed: 4 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -61,7 +61,8 @@ namespace flrd
6161
void SetFilterSize(const fluo::Vector& size);
6262
void SetCrop(bool crop);
6363
void SetNegMask(bool bval);
64-
void SetClipRotation(const fluo::Quaternion &q);
64+
void SetUseClipbox(bool bval);
65+
void SetRotation(const fluo::Quaternion &q);
6566
void SetCenter(const fluo::Point &p);
6667
void SetTranslate(const fluo::Vector &t);
6768
void Resize(SampDataType type, bool replace);
@@ -86,15 +87,10 @@ namespace flrd
8687
//crop size (of new size)
8788
fluo::Point m_crop_origin;
8889
fluo::Vector m_crop_size;
89-
//int m_ox;
90-
//int m_oy;
91-
//int m_oz;
92-
//int m_lx;
93-
//int m_ly;
94-
//int m_lz;
9590
//transform
9691
bool m_neg_mask;//use negative transformation for mask
97-
fluo::Quaternion m_q_cl;//rotation
92+
bool m_use_clipbox;//use transformation from volume clipping box
93+
fluo::Quaternion m_q;//rotation
9894
fluo::Point m_center;//rotation center
9995
fluo::Vector m_trans;//translate
10096

@@ -118,9 +114,6 @@ namespace flrd
118114
double SampleBiLinear(const fluo::Point& coord);
119115
double SampleTriLinear(const fluo::Point& coord);
120116
double SampleBox(const fluo::Point& coord);
121-
int rotate_scale(fluo::Vector &vsize_in, fluo::Vector &vspc_in,
122-
fluo::Vector &vsize, fluo::Vector &vspc);
123-
int consv_volume(fluo::Vector &vec, fluo::Vector &vec_in);
124117
bool normalize_ijk(fluo::Point& ijk);
125118
fluo::Point xyz2ijk(const fluo::Point& coord);
126119
std::pair<fluo::Point, fluo::Vector> xyz2ijkt(const fluo::Point& coord);

‎FluoRender/FluoRender/Flui/ListPanel.cpp‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -511,6 +511,7 @@ void ListPanel::SaveSelection()
511511
vd->Save(filename, fopendlg.GetFilterIndex(), 3, false,
512512
glbin_settings.m_save_crop, glbin_settings.m_save_filter,
513513
false, glbin_settings.m_save_compress,
514+
glbin_settings.m_save_crop,
514515
fluo::Point(), q, fluo::Vector(), false);
515516
std::wstring str = vd->GetPath();
516517
m_datalist->SetText(item, 2, str);
@@ -593,6 +594,7 @@ void ListPanel::BakeSelection()
593594
vd->Save(filename, fopendlg.GetFilterIndex(), 3, false,
594595
glbin_settings.m_save_crop, glbin_settings.m_save_filter,
595596
true, glbin_settings.m_save_compress,
597+
glbin_settings.m_save_crop,
596598
fluo::Point(), q, fluo::Vector(), false);
597599
std::wstring str = vd->GetPath();
598600
m_datalist->SetText(item, 2, str);

‎FluoRender/FluoRender/Project/Project.cpp‎

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1338,9 +1338,13 @@ void Project::Save(const std::wstring& filename, bool inc)
13381338
MkDirW(new_folder);
13391339
std::filesystem::path p(new_folder);
13401340
p /= vd->GetName() + L".tif";
1341-
vd->Save(p.wstring(), 0, 3, false,
1342-
false, 0, false, glbin_settings.m_save_compress,
1343-
fluo::Point(), fluo::Quaternion(), fluo::Vector(), false);
1341+
vd->Save(p.wstring(), 0,
1342+
3, false,
1343+
false, 0,
1344+
false, glbin_settings.m_save_compress,
1345+
false,
1346+
fluo::Point(), fluo::Quaternion(), fluo::Vector(),
1347+
false);
13441348
fconfig->Write("path", p.wstring());
13451349
new_chan = true;
13461350
}

‎FluoRender/FluoRender/Scene/VolumeData.cpp‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1436,6 +1436,7 @@ void VolumeData::Save(const std::wstring &filename, int mode,
14361436
int mask, bool neg_mask,
14371437
bool crop, int filter,
14381438
bool bake, bool compress,
1439+
bool use_clipbox,
14391440
const fluo::Point &c,//rotation center
14401441
const fluo::Quaternion &q,//rotation
14411442
const fluo::Vector &t,//translate
@@ -1463,7 +1464,8 @@ void VolumeData::Save(const std::wstring &filename, int mode,
14631464
sampler.SetFilterSize(fluo::Vector(1.0));
14641465
sampler.SetCrop(crop);
14651466
sampler.SetCenter(c);
1466-
sampler.SetClipRotation(q);
1467+
sampler.SetUseClipbox(use_clipbox);
1468+
sampler.SetRotation(q);
14671469
sampler.SetTranslate(t);
14681470
sampler.SetNegMask(neg_mask);
14691471
bool replace = temp ? true : false;

‎FluoRender/FluoRender/Scene/VolumeData.h‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -137,6 +137,7 @@ class VolumeData : public TreeLayer, public std::enable_shared_from_this<VolumeD
137137
int mask, bool neg_mask,
138138
bool crop, int filter,
139139
bool bake, bool compress,
140+
bool use_clipbox,
140141
const fluo::Point &c,
141142
const fluo::Quaternion &q,
142143
const fluo::Vector &t,

‎FluoRender/FluoRender/Script/ScriptProc.cpp‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1108,6 +1108,7 @@ void ScriptProc::RunSaveVolume()
11081108
mask, neg_mask,
11091109
crop, filter,
11101110
bake, compression,
1111+
false,
11111112
center, rot, transl,
11121113
fix_size);
11131114
}

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