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imagej-elphel
Commit a47aabbe authored by Andrey Filippov's avatar Andrey Filippov
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Linear output for GRAY32 GEO output, UM for ARGB (slow fillNaNs)

parent 24d7049d
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Showing with 238 additions and 87 deletions
src/main/java/com/elphel/imagej/cameras/CLTParameters.java
View file @ a47aabbe
......@@ -489,7 +489,14 @@ public class CLTParameters {
public boolean gmap_save_alt = true; // save height map (meters ASL)
public boolean gmap_save_tiff32 = true; // save float TIFF (NaN for transparency) with geo metadata (top left corner)
public boolean gmap_save_tiff = true; // save transparent TIFF with geo metadata (top left corner)
public int gmap_tiff_pal = 0; // LWIR palette for TIFF
public int gmap_tiff_pal = 0; // LWIR palette for ARGB TIFF
public boolean gmap_um = true; // Use unsharp mask filter for ARGB TIFF maps
public double gmap_um_sigma = 0.4; // Unsharp mask sigma for ARGB TIFF maps (in meters)
public double gmap_um_weight = 0.8; // Unsharp mask weight for ARGB TIFF maps
public boolean gmap_lwir_autorange = true; // Autorange LWIR textures for ARGB TIFF maps
public boolean gmap_um_fixed = false; // Use fixed range after unsharp mask instead of autorange for ARGB TIFF maps
public double gmap_um_range = 500; // Full range after unsharp mask for ARGB TIFF maps
public boolean generate_bg = true; // Generate background image for 3dmodels
public boolean show_textures = true; // show generated textures
......@@ -1639,6 +1646,13 @@ public class CLTParameters {
properties.setProperty(prefix+"gmap_save_tiff32", this.gmap_save_tiff32+""); // boolean
properties.setProperty(prefix+"gmap_save_tiff", this.gmap_save_tiff+""); // boolean
properties.setProperty(prefix+"gmap_tiff_pal", this.gmap_tiff_pal+""); // int
properties.setProperty(prefix+"gmap_um", this.gmap_um+""); // boolean
properties.setProperty(prefix+"gmap_um_sigma", this.gmap_um_sigma+""); // double
properties.setProperty(prefix+"gmap_um_weight", this.gmap_um_weight+""); // double
properties.setProperty(prefix+"gmap_lwir_autorange", this.gmap_lwir_autorange+""); // boolean
properties.setProperty(prefix+"gmap_um_fixed", this.gmap_um_fixed+""); // boolean
properties.setProperty(prefix+"gmap_um_range", this.gmap_um_range+""); // double
properties.setProperty(prefix+"generate_bg", this.generate_bg+"");
properties.setProperty(prefix+"show_textures", this.show_textures+"");
......@@ -2663,6 +2677,13 @@ public class CLTParameters {
if (properties.getProperty(prefix+"gmap_save_tiff32")!=null) this.gmap_save_tiff32=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff32"));
if (properties.getProperty(prefix+"gmap_save_tiff")!=null) this.gmap_save_tiff=Boolean.parseBoolean(properties.getProperty(prefix+ "gmap_save_tiff"));
if (properties.getProperty(prefix+"gmap_tiff_pal")!=null) this.gmap_tiff_pal=Integer.parseInt(properties.getProperty(prefix+ "gmap_tiff_pal"));// int
if (properties.getProperty(prefix+"gmap_um")!=null) this.gmap_um=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_um"));
if (properties.getProperty(prefix+"gmap_um_sigma")!=null) this.gmap_um_sigma=Double.parseDouble(properties.getProperty(prefix+"gmap_um_sigma"));
if (properties.getProperty(prefix+"gmap_um_weight")!=null) this.gmap_um_weight=Double.parseDouble(properties.getProperty(prefix+"gmap_um_weight"));
if (properties.getProperty(prefix+"gmap_lwir_autorange")!=null) this.gmap_lwir_autorange=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_lwir_autorange"));
if (properties.getProperty(prefix+"gmap_um_fixed")!=null) this.gmap_um_fixed=Boolean.parseBoolean(properties.getProperty(prefix+"gmap_um_fixed"));
if (properties.getProperty(prefix+"gmap_um_range")!=null) this.gmap_um_range=Double.parseDouble(properties.getProperty(prefix+"gmap_um_range"));
if (properties.getProperty(prefix+"generate_bg")!=null) this.generate_bg=Boolean.parseBoolean(properties.getProperty(prefix+"generate_bg"));
if (properties.getProperty(prefix+"show_textures")!=null) this.show_textures=Boolean.parseBoolean(properties.getProperty(prefix+"show_textures"));
......@@ -3939,8 +3960,24 @@ public class CLTParameters {
"Save float (32-bit) TIFF with geo and resolution metadata (coordinates correspond to the top left image corner), NAN for transparency.");
gd.addCheckbox ("Save ARGB Tiff with transparency and Geo",this.gmap_save_tiff, // true; // enable change FG pixel to opaque from transparent
"Save transparent TIFF with geo and resolution metadata (coordinates correspond to the top left image corner).");
gd.addNumericField("Crop maps extra", this.gmap_tiff_pal, 0,3,"", // minimal neighbors to keep alpha
gd.addNumericField("LWIR palette for Geo", this.gmap_tiff_pal, 0,3,"", // minimal neighbors to keep alpha
"LWIR palette for Geo/transparency TIFF output.");
gd.addMessage ("Unsharp mask parameters for ARGB render of the ground maps");
gd.addCheckbox ("Apply unsharp mask to ARGB render", this.gmap_um,
"Use unsharp mask filter for texture.");
gd.addNumericField("Unsharp mask sigma", this.gmap_um_sigma, 5,7,"m",
"Unsharp mask sigma for ARGB ground map render in meters.");
gd.addNumericField("Unsharp mask weight", this.gmap_um_weight, 5,7,"",
"Unsharp mask weight for ARGB ground map render.");
gd.addCheckbox ("Autorange LWIR textures", this.gmap_lwir_autorange,
"Autorange LWIR ARGB ground map render (after unsharp mask).");
gd.addCheckbox ("Fixed range (after unsharp only)", this.gmap_um_fixed,
"Use fixed range after unsharp mask for ARGB ground map instead of autorange.");
gd.addNumericField("Full range for ARGB ground map render",this.gmap_um_range, 5,7,"counts",
"Full range after unsharp mask when fixed range is selected.");
gd.addMessage ("Earlier 3D generation parameters");
gd.addCheckbox ("Generate background (infinity) image for 3D (not needed for view down)", this.generate_bg);
......@@ -5159,10 +5196,17 @@ public class CLTParameters {
this.gmap_tex_pals = CLTParameters.str_to_iarr(gd.getNextString());
this.gmap_save_alt= gd.getNextBoolean();
this.gmap_save_tiff32= gd.getNextBoolean();
this.gmap_save_tiff32= gd.getNextBoolean();
this.gmap_save_tiff= gd.getNextBoolean();
this.gmap_tiff_pal= (int) gd.getNextNumber();
this.gmap_um = gd.getNextBoolean();
this.gmap_um_sigma = gd.getNextNumber();
this.gmap_um_weight = gd.getNextNumber();
this.gmap_lwir_autorange = gd.getNextBoolean();
this.gmap_um_fixed = gd.getNextBoolean();
this.gmap_um_range = gd.getNextNumber();
this.generate_bg= gd.getNextBoolean();
this.show_textures= gd.getNextBoolean();
this.debug_filters= gd.getNextBoolean();
......
src/main/java/com/elphel/imagej/readers/ElphelTiffWriter.java
View file @ a47aabbe
......@@ -194,13 +194,13 @@ public class ElphelTiffWriter {
int bands = 1; // 4 bands for ARGB, 3 for RGB etc
int[] bandOffsets = {0}; // length == bands, 0 == R, 1 == G, 2 == B and 3 == A
// Create a TYPE_FLOAT sample model (specifying how the pixels are stored)
SampleModel sampleModel0 = new PixelInterleavedSampleModel(
DataBuffer.TYPE_FLOAT,
width,
height,
bands,
width * bands,
bandOffsets);
// SampleModel sampleModel0 = new PixelInterleavedSampleModel(
// DataBuffer.TYPE_FLOAT,
// width,
// height,
// bands,
// width * bands,
// bandOffsets);
// Create a color model compatible with this sample model/raster (TYPE_FLOAT)
// Note that the number of bands must equal the number of color components in the
......
src/main/java/com/elphel/imagej/tileprocessor/QuadCLTCPU.java
View file @ a47aabbe
......@@ -8668,7 +8668,7 @@ public class QuadCLTCPU {
double [][][] textures // [nslices][nchn][i]
) {
if ((textures == null) || (textures.length==0)) {
throw new IllegalArgumentException ("umTextures(): Empty textures");
throw new IllegalArgumentException ("getMinMaxTextures(): Empty textures");
}
final boolean is_mono = textures[0].length <= 2;
final int alpha_chn = is_mono? 1 : 3;
......@@ -16456,6 +16456,52 @@ public class QuadCLTCPU {
return true;
}
// Currently only a single-slice 32-bit file (with NaN for tranparency)
public boolean writeLwirGeoTiff32(
final CLTParameters clt_parameters,
double [] data,
double [] lla, // latitude, longitude, altitude (or null)
LocalDateTime dt, // local date/time or null
double pix_in_meters,
int width,
QuadCLT scene,
String suffix, // include "-geo"
int debugLevel) {
if (scene == null) {
scene = (QuadCLT) this;
}
int height = data.length/width;
String set_name = getImageName();
if (set_name == null ) {
QuadCLTCPU.SetChannels [] set_channels = setChannels(debugLevel);
set_name = set_channels[0].set_name;
}
String model_dir= correctionsParameters.selectX3dDirectory(
set_name, // quad timestamp. Will be ignored if correctionsParameters.use_x3d_subdirs is false
null,
true, // smart,
true); //newAllowed, // save\
String title = getImageName()+suffix;
ImagePlus imp = ShowDoubleFloatArrays.makeArrays(
data, // double[] pixels,
width, // int width,
height, // int height,
title); // String title);
String image_path = model_dir + Prefs.getFileSeparator() + title+".tiff";
ElphelTiffWriter.saveTiffARGBOrGray32(
imp,
image_path,
lla, // double [] lla, // latitude, longitude, altitude (or null)
dt, // LocalDateTime dt, // local date/time or null
pix_in_meters, //double pix_in_meters, // resolution or Double.NaN
false, // imageJTags,
debugLevel);
return true;
}
/** broke
public boolean writeRatingFile( // USED in lwir
......
src/main/java/com/elphel/imagej/tileprocessor/TexturedModel.java
View file @ a47aabbe
......@@ -2471,9 +2471,15 @@ public class TexturedModel {
final int crop_extra = clt_parameters.gmap_crop_extra ; //20;
final int [] tex_pals = clt_parameters.gmap_tex_pals ; //{0,1,2};
final boolean gmap_save_alt = clt_parameters.gmap_save_alt; // true; // save height map (meters ASL)
final boolean gmap_save_tiff32= clt_parameters.gmap_save_tiff32; // save float TIFF (NaN for transparency) with geo metadata (top left corner)
final boolean gmap_save_tiff = clt_parameters.gmap_save_tiff; // true; // save transparent TIFF with geo metadata (top left corner)
final int gmap_tiff_pal = clt_parameters.gmap_tiff_pal; // 0; // LWIR palette for TIFF
final boolean gmap_um = clt_parameters.gmap_um; // true; // Use unsharp mask filter for ARGB TIFF maps
final double gmap_um_sigma = clt_parameters.gmap_um_sigma; // 0.4; // Unsharp mask sigma for ARGB TIFF maps (in meters)
final double gmap_um_weight = clt_parameters.gmap_um_weight; // 0.8; // Unsharp mask weight for ARGB TIFF maps
final boolean gmap_lwir_autorange = clt_parameters.gmap_lwir_autorange;// true; // Autorange LWIR textures for ARGB TIFF maps
final boolean gmap_um_fixed = clt_parameters.gmap_um_fixed; // false; // Use fixed range after unsharp mask instead of autorange for ARGB TIFF maps
final double gmap_um_range = clt_parameters.gmap_um_range; // 500; // Full range after unsharp mask for ARGB TIFF maps
final double range_disparity_offset = clt_parameters.imp.range_disparity_offset;// double range_disparity_offset
final boolean batch_mode = clt_parameters.multiseq_run; // batch_run;
......@@ -3068,9 +3074,6 @@ public class TexturedModel {
}
// String model_name = ref_scene.correctionsParameters.getModelName(ref_scene.getImageName());
String suffix ="-RECT";
if (clt_parameters.tex_um) {
suffix+="-UM"+(clt_parameters.tex_um_sigma)+"_"+(clt_parameters.tex_um_weight);
}
suffix +="-PIX"+pix_size * hdr_whs[2];
scenes[ref_index].saveDoubleArrayInModelDirectory(
suffix+"-FULL", // String suffix,
......@@ -3136,44 +3139,102 @@ public class TexturedModel {
}
}
double avg_z = sum_z/num_pix;
LocalDateTime dt = scenes[ref_index].getLocalDateTime();
top_left_lla[2] = avg_z; // average altitude. Maybe keep drone altitude?
if (gmap_save_alt) {
/*
scenes[ref_index].saveDoubleArrayInTopModelDirectory( // save with Z
suffix+"-ALT", // String suffix,
null, // String [] labels, // or null
new double[][] {cropped_z[0]}, // double [][] data,
hdr_whs[0], // int width, // int tilesX,
hdr_whs[1]); // int height, // int tilesY,
*/
scenes[ref_index].writeLwirGeoTiff32(
clt_parameters, // final CLTParameters clt_parameters,
cropped_z[0], // double [] data,
top_left_lla, // double [] lla, // latitude, longitude, altitude (or null)
dt, // LocalDateTime dt, // local date/time or null
scaled_pixel_size, // double pix_in_meters,
hdr_whs[0], // int width,
null, // QuadCLT scene,
suffix+"-GEO-ALT", // String suffix,
debugLevel); // int debugLevel)
}
double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
if (gmap_save_tiff && (gmap_tiff_pal >=0)) {
LocalDateTime dt = scenes[ref_index].getLocalDateTime();
scenes[ref_index].writeLwirGeoTiffARGB(
if (gmap_save_tiff32) {
scenes[ref_index].writeLwirGeoTiff32(
clt_parameters, // final CLTParameters clt_parameters,
img_cropped[0], // double [] data,
img_cropped[0], // double [] data,
top_left_lla, // double [] lla, // latitude, longitude, altitude (or null)
dt, // LocalDateTime dt, // local date/time or null
scaled_pixel_size, // double pix_in_meters,
hdr_whs[0], // int width,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
gmap_tiff_pal, // int tex_palette,
suffix+"-GEO"+"-PAL"+gmap_tiff_pal, // String suffix,
suffix+"-GEO", // String suffix,
debugLevel); // int debugLevel)
}
for (int tex_palette: tex_pals) {
// try with fixed range?
// double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
scenes[ref_index].writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
img_cropped[0], // double [] data,
hdr_whs[0], // int width,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
suffix+"-CROP"+"-PAL"+tex_palette, // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
if ((gmap_save_tiff && (gmap_tiff_pal >=0)) || (tex_pals.length > 0)) {
// TODO: Move UM here, save 32-bit GEO w/o UM
if (gmap_um) {
double um_sigma = gmap_um_sigma / scaled_pixel_size;
int grow_pix = (int) (4 * um_sigma); // experimentally - UM grows by 4*sigma;
// it is needed before Gaussian blur which extends NaN
double [] um_data = TileProcessor.fillNaNs(
img_cropped[0], // final double [] data,
null, // final boolean [] prohibit,
hdr_whs[0], // int width,
// CAREFUL ! Remaining NaN is grown by unsharp mask filter ************* !
2*grow_pix, // 2*width, // 16, // final int grow,
0.7, // double diagonal_weight, // relative to ortho
100, // int num_passes,
0.03, // final double max_rchange, // = 0.01 - does not need to be accurate
THREADS_MAX); // final int threadsMax) // maximal number of threads to launch
double [][][] um_data3 = {{um_data}};
QuadCLTCPU.umTextures(
um_data3, // final double [][][] textures, // [nslices][nchn][i]
hdr_whs[0], // tilesX * transform_size, // final int width,
false, // um_ignore_alpha, // final boolean ignore_alpha,
um_sigma, // final double um_sigma,
gmap_um_weight); // final double um_weight)
for (int i = 0; i < um_data.length; i++) {
if (Double.isNaN(img_cropped[0][i])) {
um_data[i] = Double.NaN;
}
}
img_cropped[0] = um_data; // replaced with UM
suffix+="-UM"+(clt_parameters.tex_um_sigma)+"_"+(clt_parameters.tex_um_weight);
}
double [] minmax = gmap_um_fixed ? (new double[] {-gmap_um_range/2, gmap_um_range/2}): null;
if (gmap_save_tiff && (gmap_tiff_pal >=0)) {
scenes[ref_index].writeLwirGeoTiffARGB(
clt_parameters, // final CLTParameters clt_parameters,
img_cropped[0], // double [] data,
top_left_lla, // double [] lla, // latitude, longitude, altitude (or null)
dt, // LocalDateTime dt, // local date/time or null
scaled_pixel_size, // double pix_in_meters,
hdr_whs[0], // int width,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
gmap_tiff_pal, // int tex_palette,
suffix+"-GEO"+"-PAL"+gmap_tiff_pal, // String suffix,
debugLevel); // int debugLevel)
}
for (int tex_palette: tex_pals) {
// try with fixed range?
// double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
scenes[ref_index].writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
img_cropped[0], // double [] data,
hdr_whs[0], // int width,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
suffix+"-CROP"+"-PAL"+tex_palette, // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
}
}
}
......@@ -7593,18 +7654,7 @@ public class TexturedModel {
tilesX * transform_size, // int width, // int tilesX,
tilesY * transform_size); // int height, // int tilesY,
}
// Optionally apply UM (before auto/manual range)
final boolean um_ignore_alpha = true;
final boolean hist_ignore_alpha = true;
if (tex_um) {
QuadCLTCPU.umTextures(
faded_textures, // final double [][][] textures, // [nslices][nchn][i]
tilesX * transform_size, // final int width,
um_ignore_alpha, // final boolean ignore_alpha,
tex_um_sigma, // final double um_sigma,
tex_um_weight); // final double um_weight)
}
// save linear textures before applying UM
if (lin_textures != null) {
// duplicate texture before normalization
lin_textures[0] = new double [faded_textures.length][][];
......@@ -7619,6 +7669,17 @@ public class TexturedModel {
}
}
}
// Optionally apply UM (before auto/manual range)
final boolean um_ignore_alpha = true;
final boolean hist_ignore_alpha = true;
if (tex_um) {
QuadCLTCPU.umTextures(
faded_textures, // final double [][][] textures, // [nslices][nchn][i]
tilesX * transform_size, // final int width,
um_ignore_alpha, // final boolean ignore_alpha,
tex_um_sigma, // final double um_sigma,
tex_um_weight); // final double um_weight)
}
if (save_interm_textures || save_um_texture0) {
double [][] dbg_textures = new double [faded_textures.length * faded_textures[0].length][faded_textures[0][0].length];
String [] dbg_titles = new String[dbg_textures.length];
......@@ -7758,45 +7819,45 @@ public class TexturedModel {
dbg_textures[i] = faded_textures[i / faded_textures[0].length][i % faded_textures[0].length];
dbg_titles[i] = dbg_subtitles[i % dbg_subtitles.length] + "-" + (i / dbg_subtitles.length);
}
if (save_preview) {
// final boolean tex_um_fixed = clt_parameters.tex_um_fixed; // imp.mono_fixed; // true; // normalize to fixed range when converting to 8 bits
// final double tex_um_range = clt_parameters.tex_um_range; // imp.mono_range; // 500.0; // monochrome full-scale range (+/- half)
double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
/*
ref_scene.writePreview( // may move to different (earlier) stage of processing, (search for "-combined_textures")
dbg_textures[0], // double [] data,
debugLevel); // int debugLevel
*/
// Trying different palettes
int tex_palette = 0; // regular mono white-hot
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
tex_palette = 1; // regular color
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"-black_hot", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
tex_palette = 2; // regular color
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"-color", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
}
if (save_preview) {
// final boolean tex_um_fixed = clt_parameters.tex_um_fixed; // imp.mono_fixed; // true; // normalize to fixed range when converting to 8 bits
// final double tex_um_range = clt_parameters.tex_um_range; // imp.mono_range; // 500.0; // monochrome full-scale range (+/- half)
double [] minmax = tex_um_fixed ? (new double[] {-tex_um_range/2, tex_um_range/2}): null;
/*
ref_scene.writePreview( // may move to different (earlier) stage of processing, (search for "-combined_textures")
dbg_textures[0], // double [] data,
debugLevel); // int debugLevel
*/
// Trying different palettes
int tex_palette = 0; // regular mono white-hot
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
tex_palette = 1; // regular color
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"-black_hot", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
tex_palette = 2; // regular color
ref_scene.writeLwirPreview(
clt_parameters, // final CLTParameters clt_parameters,
dbg_textures[0], // double [] data,
minmax, // double [] minmax, // null for auto
null, // QuadCLT scene,
tex_palette, // int tex_palette,
"-color", // +tex_palette, // String suffix,
debugLevel); // int debugLevel)
}
if (save_interm_textures) {
String suffix = "-combined_textures";
if (!batch_run && (debugLevel > -1)) {
......
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