merging with master

.gitattributes

+*.cu gitlab-language=cpp
+*.cuh gitlab-language=cpp
\ No newline at end of file

README.md

 This is a set of Elphel plugins for ImageJ 1.x as a Maven project with specified
-dependencies,
+dependencies.
 If cloned and imported as existent Maven project into Eclipse IDE, it allows to launch
 ImageJ with plugins in both run and debug modes.
 

src/main/java/com/elphel/imagej/correction/EyesisCorrections.java

@@ -742,7 +742,7 @@ public class EyesisCorrections {
 			if (path!=null){
 				path+=Prefs.getFileSeparator()+imp.getTitle()+".tiff";
 	 			 if (this.debugLevel>0) System.out.println("Saving equirectangular result to "+path);
-				(new EyesisTiff()).saveTiff(
+				(new EyesisTiff(correctionsParameters.tiffCompression)).saveTiff(
 						imp,
 						path,
 						correctionsParameters.equirectangularFormat,

src/main/java/com/elphel/imagej/jp4/JP46_Reader_camera.java

@@ -23,30 +23,26 @@
  ** -----------------------------------------------------------------------------**
  **
  */
+//from main
 package com.elphel.imagej.jp4;
-import java.awt.Button;
-import java.awt.Frame;
-import java.awt.GridLayout;
-import java.awt.Image;
-import java.awt.Panel;
-import java.awt.Rectangle;
-import java.awt.Toolkit;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.RandomAccessFile;
-import java.io.StringReader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLConnection;
+
+import ij.*;
+import ij.io.*;
+import ij.process.*;
+import ij.gui.*;
+import ij.plugin.frame.*;
+import ij.text.*;
+import ij.plugin.PlugIn;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.net.*;
 import java.util.Iterator;
 import java.util.Properties;
 import java.util.Set;
+import java.io.*;
 
-import javax.swing.JFileChooser;
+import javax.swing.*;
 import javax.xml.parsers.DocumentBuilder;
 import javax.xml.parsers.DocumentBuilderFactory;
 import javax.xml.parsers.ParserConfigurationException;
@@ -56,25 +52,11 @@ import org.w3c.dom.NodeList;
 import org.xml.sax.InputSource;
 import org.xml.sax.SAXException;
 
-import ij.IJ;
-import ij.ImageJ;
-import ij.ImagePlus;
-import ij.ImageStack;
-import ij.Prefs;
-import ij.WindowManager;
-import ij.gui.GUI;
-import ij.gui.GenericDialog;
-import ij.io.FileInfo;
-import ij.io.OpenDialog;
-import ij.plugin.frame.PlugInFrame;
-import ij.process.ImageConverter;
-import ij.process.ImageProcessor;
-import ij.text.TextWindow;
 
 
 
 /* This plugin opens images in Elphel JP4/JP46 format (opens as JPEG, reads MakerNote and converts). */
-public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
+public class JP46_Reader_camera implements PlugIn, ActionListener {
 
 	/**
 	 *
@@ -83,6 +65,7 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 	Panel panel1;
 	Panel confpanel;
 	Frame instance;
+	PlugInFrame plugInFrame; 
 
 	String arg;
 
@@ -97,44 +80,31 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
     public boolean demux=true;
 	public String imageTitle="cameraImage";
 	private int ExifOffset=0x0c;
+	private Boolean headless=GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadlessInstance(); 
 
-	public JP46_Reader_camera() {
-		super("JP46 Reader Camera");
-		if (IJ.versionLessThan("1.39t")) return;
-		if (instance!=null) {
-			instance.toFront();
-			return;
+	public void run(String arg) {
 		}
-		instance = this;
-		addKeyListener(IJ.getInstance());
-
-		panel1 = new Panel();
 
-		panel1.setLayout(new GridLayout(6, 1, 50, 5));
-
-		addButton("Open JP4/JP46...",panel1);
-		addButton("Open JP4/JP46 from camera",panel1);
-		addButton("Configure...",panel1);
-		addButton("Show image properties",panel1);
-		addButton("Decode image info to properties",panel1);
-		addButton("Split Bayer",panel1);
+	public JP46_Reader_camera(Boolean showGui) {
+		if (showGui) initGui();
+	}
 
+	public JP46_Reader_camera() {
+		initGui();
+	}
 
-		add(panel1);
+	private void initGui() {
+		if (headless) return;
 
-		pack();
-		GUI.center(this);
-		setVisible(true);
-	}
-	public JP46_Reader_camera(boolean showGUI) {
-		super("JP46 Reader Camera");
 		if (IJ.versionLessThan("1.39t")) return;
 		if (instance!=null) {
 			instance.toFront();
 			return;
 		}
-		instance = this;
-		addKeyListener(IJ.getInstance());
+		plugInFrame=new PlugInFrame("JP46 Reader Camera");
+		instance = (Frame)plugInFrame;
+
+		plugInFrame.addKeyListener(IJ.getInstance());
 
 		panel1 = new Panel();
 
@@ -146,15 +116,14 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		addButton("Show image properties",panel1);
 		addButton("Decode image info to properties",panel1);
 		addButton("Split Bayer",panel1);
-		add(panel1);
-		pack();
-		GUI.center(this);
-		setVisible(showGUI);
-		if (!showGUI) {
-			this.ABSOLUTELY_SILENT = true;
-		}
-	}
 
+
+		plugInFrame.add(panel1);
+
+		plugInFrame.pack();
+		GUI.center(plugInFrame);
+		plugInFrame.setVisible(true);
+	}
 	void addButton(String label, Panel panel) {
 		Button b = new Button(label);
 		b.addActionListener(this);
@@ -162,7 +131,6 @@ public class JP46_Reader_camera extends PlugInFrame implements ActionListener {
 		panel.add(b);
 	}
 
-	@Override
 	public void actionPerformed(ActionEvent e) {
 		String label = e.getActionCommand();
 
@@ -1434,13 +1402,7 @@ Exception in thread "Thread-3564" java.lang.ArrayIndexOutOfBoundsException: 8970
 		Class<?> clazz = JP46_Reader_camera.class;
 		String url = clazz.getResource("/" + clazz.getName().replace('.', '/') + ".class").toString();
 		String pluginsDir = url.substring(5, url.length() - clazz.getName().length() - 6);
-		System.out.println(System.getProperty("plugins.dir"));
-
 		System.setProperty("plugins.dir", pluginsDir);
-//		System.setProperty("plugins.dir", "/data_ssd/imagej-elphel/ijplugins");
-//		System.setProperty("plugins.dir", "/data_ssd/imagej-elphel/target/classes/com/elphel/imagej/jp4/");
-		System.out.println(System.getProperty("plugins.dir"));
-
 		// start ImageJ
 		new ImageJ();
 		// run the plugin

src/main/resources/escher_pattern.py

+#!/usr/bin/env python3
+
+'''
+/**
+ * @file escher_pattern.py
+ * @brief wrapper for web
+ * @par <b>License</b>:
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+'''
+
+from urllib.parse import urlparse, parse_qs
+
+import time
+
+# this is needed for importing?
+import os, sys
+os.chdir(os.path.dirname(__file__))
+sys.path.append(os.path.dirname(__file__))
+# also add:
+'''
+/etc/apache2/conf-enabled/serve-cgi-bin.conf:
+                <Directory /var/www/html/pytest>
+                        Options +ExecCGI
+                        AddHandler wsgi-script .py
+                        WSGIProcessGroup %{GLOBAL}
+                        WSGIApplicationGroup %{GLOBAL}
+                        Order deny,allow
+                        Allow from all
+                </Directory>
+
+'''
+
+from escher_pattern_class import Escher_Pattern
+
+# def application is a hardcoded keyword for WSGI ?!
+def application(environ,start_response):
+
+    params = parse_qs(environ["QUERY_STRING"])
+
+    status = '200 OK'
+
+    lpm = 50
+    page_width  = 270
+    page_height = 210
+    rotate = 5
+    escher = 2.0
+    tmp_dir = 'tmp'
+
+    try:
+      lpm = float(params['LPM'][0])
+    except KeyError:
+      pass
+
+    try:
+      page_width = float(params['PAGE_WIDTH'][0])
+    except KeyError:
+      pass
+
+    try:
+      page_height = float(params['PAGE_HEIGHT'][0])
+    except KeyError:
+      pass
+
+    try:
+      rotate = float(params['ROTATE'][0])
+    except KeyError:
+      pass
+
+    try:
+      escher = float(params['ESCHER'][0])
+    except KeyError:
+      pass
+
+    basename  = 'escher-pattern'
+    basename += '-ESCHER'+str(escher)
+    basename += '-LPM'+str(lpm)
+    basename += '-ROT'+str(rotate)
+    basename += '-PAGE_WIDTH'+str(page_width)
+    basename += '-PAGE_HEIGHT'+str(page_height)
+    pdf_name  = basename+".pdf"
+
+    ep = Escher_Pattern(width= page_width, height= page_height, escher=escher, lpm=lpm, rotate=rotate)
+    ep.generate()
+    ep.save()
+
+    with open(pdf_name,'rb') as f:
+      contents = f.read()
+
+    os.remove(pdf_name)
+
+    filesize = str(len(contents))
+    filesize = filesize.encode('utf-8')
+
+    response_header = [
+      ('Content-Type','application/pdf'),
+      ('Cache-Control', 'public, must-revalidate, max-age=0'),
+      ('Pragma', 'public'),
+      ('Expires', 'Sat, 26 Jul 1997 05:00:00 GMT'),
+      ('Last-Modified', time.strftime("%a, %d %b %Y %H:%M:%S GMT", time.gmtime())),
+      ('Content-Length', str(len(contents))),
+      ('Content-Disposition', 'inline; filename='+pdf_name+';')
+    ]
+
+    start_response(status,response_header)
+
+    return [contents]

src/main/resources/escher_pattern_class.py

+#!/usr/bin/env python3
+
+'''
+/**
+ * @file escher_pattern_class.py
+ * @brief escher pattern generator
+ * @par <b>License</b>:
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public License
+ *  along with this program.  If not, see <http://www.gnu.org/licenses/>.
+*/
+'''
+
+import matplotlib.pyplot as plt
+from matplotlib.backends.backend_pdf import PdfPages
+
+import numpy as np
+
+from matplotlib.patches import Arc
+from matplotlib.patches import Circle
+from matplotlib.patches import Rectangle
+from matplotlib.patches import Polygon
+from matplotlib.patches import Wedge
+from matplotlib.patches import PathPatch
+
+import matplotlib as mpl
+
+from matplotlib import collections
+from matplotlib.path import Path
+
+import copy
+import math
+
+import sys
+
+'''
+requirements:
+  
+  - matplotlib, version 3.0.3
+  - BUG?: matplotlib, version 2.0.2 draws a little padding around which is not desired
+
+install:
+
+  - sudo pip3 install matplotlib
+  - sudo apt install python3-tk
+  
+'''
+
+class Escher_Pattern:
+
+  # units are mms but coordinates are in pt to compare with php script
+  MM2PT = 72.0/25.4
+  opts_k = {'facecolor':'black','edgecolor':'r','linewidth':0}
+  opts_w = {'facecolor':'white','edgecolor':'r','linewidth':0}
+  opts_b = {'facecolor':'blue', 'edgecolor':'r','linewidth':0}
+  opts_r = {'facecolor':'red', 'edgecolor':'r','linewidth':0}
+
+  # init
+  def __init__(self,
+               width    = 270,  # width in units
+               height   = 210,  # height in units
+               lpm      = 50,   # lines per meter
+               escher   = 2.0,  # curvature coefficient
+               rotate   = 5,    # degrees
+               units    = 'mm',
+               ):
+
+    self.width    = int(width*self.MM2PT)
+    self.height   = int(height*self.MM2PT)
+    self.lpm      = lpm
+    self.escher   = escher
+    self.angle   = rotate
+    self.units = units
+
+    self.basename = 'escher-pattern'
+    self.basename += '-ESCHER'+str(self.escher)
+    self.basename += '-LPM'+str(self.lpm)
+    self.basename += '-ROT'+str(self.angle)
+    self.basename += '-PAGE_WIDTH'+str(width)
+    self.basename += '-PAGE_HEIGHT'+str(height)
+
+    self.pdf_name = self.basename+".pdf"
+
+    plt.autoscale(tight=True)
+    plt.axis('off')
+    plt.margins(0.0)
+    #plt.rcParams["figure.figsize"] = [60,120]
+
+    self.fig, self.ax = plt.subplots()
+    self.fig.set_size_inches(self.width/72, self.height/72)
+
+    self.ax.get_xaxis().set_visible(False)
+    self.ax.get_yaxis().set_visible(False)
+    self.ax.set_aspect('equal')
+
+    self.ax.spines['top'].set_visible(False)
+    self.ax.spines['right'].set_visible(False)
+    self.ax.spines['left'].set_visible(False)
+    self.ax.spines['bottom'].set_visible(False)
+
+    self.ax.set_ylim([0,self.height])
+    self.ax.set_xlim([0,self.width])
+
+    self.ax.set_facecolor('white')
+
+    self.rotation = mpl.transforms.Affine2D().rotate_deg(-self.angle) + self.ax.transData
+
+    #print("init done")
+
+
+  # generate and place a patch
+  def generate_cell(self,x,y,tpts,template,halfAngle,r,ba):
+
+    for k,v in enumerate(template):
+
+      # even-even black cell
+      vcp = copy.copy(v)
+      if   (type(v)==Wedge):
+        vcp.set_center((tpts[k][0]+x,tpts[k][1]+y))
+      elif (type(v)==Rectangle):
+        vcp.set_xy((tpts[k][0]+x,tpts[k][1]+y))
+
+      self.ax.add_patch(vcp)
+      vcp.set_transform(self.rotation)
+
+      # do clipping
+      if   (type(v)==Wedge):
+
+        sin0 = math.sin(math.radians(halfAngle))
+        cos0 = math.cos(math.radians(halfAngle))
+
+        if ba[k]==0:
+          w0 = r - r*cos0
+          h0 = 2*r*sin0
+          x0 = tpts[k][0] + r - w0
+          y0 = tpts[k][1] - h0/2
+        if ba[k]==180:
+          w0 = r - r*cos0
+          h0 = 2*r*sin0
+          x0 = tpts[k][0] - r
+          y0 = tpts[k][1] - h0/2
+        if ba[k]==270:
+          w0 = 2*r*sin0
+          h0 = r - r*cos0
+          x0 = tpts[k][0] - w0/2
+          y0 = tpts[k][1] - r
+        if ba[k]==90:
+          w0 = 2*r*sin0
+          h0 = r - r*cos0
+          x0 = tpts[k][0] - w0/2
+          y0 = tpts[k][1] + r - h0
+
+
+        # correction, so the shadow line from Rectange is not seen
+        if ba[k]==0:
+          x0 -= w0
+          w0 *= 2
+        if ba[k]==180:
+          w0 *= 2
+        if ba[k]==270:
+          h0 *= 2
+        if ba[k]==90:
+          y0 -= h0
+          h0 *= 2
+
+        cp = Rectangle((x0,y0),w0,h0,**self.opts_w, lw=0)
+        vcp2 = copy.copy(cp)
+
+        xy = vcp2.get_xy()
+        vcp2.set_xy((xy[0]+x,xy[1]+y))
+        path = vcp2.get_path()
+        transform = vcp2.get_transform()
+        path = transform.transform_path(path)
+        vcp2 = PathPatch(path, fc='none', ec='none', lw=0)
+        self.ax.add_patch(vcp2)
+        # rotate here
+        vcp2.set_transform(self.rotation)
+
+        vcp.set_clip_path(vcp2)
+
+
+  # generate the whole pattern
+  def generate(self):
+
+    side = 500/self.lpm*self.MM2PT
+
+    # escher pattern
+    if (self.escher>0):
+
+      # no rounding
+      Size = side
+      qSize = Size/4
+      hSize = Size/2
+      a = self.escher*(math.sqrt(2)-1.0)
+      r = (a*a+1)/(2*a)*qSize
+      r2 = r*r
+      h = math.sqrt(r2-qSize*qSize)
+      dc = 2*qSize-h
+      halfAngle = math.degrees(math.atan(qSize/h))
+      center = dc+r
+
+      ba = [
+        None,
+        0,
+        180,
+        270,
+        90,
+        180,
+        0,
+        90,
+        270
+      ]
+
+      tpts = [
+          [center-hSize,   center-hSize],
+          [center-Size+dc, center-qSize],
+          [center-dc,      center+qSize],
+          [center-qSize,   center+Size-dc],
+          [center+qSize,   center+dc],
+          [center+Size-dc, center+qSize],
+          [center+dc,      center-qSize],
+          [center+qSize,   center-Size+dc],
+          [center-qSize,   center-dc]
+        ]
+
+      template = [
+        Rectangle( tpts[0],  Size, Size, **self.opts_k),
+        Wedge(     tpts[1],  r, ba[1]-halfAngle, ba[1]+halfAngle, **self.opts_w),
+        Wedge(     tpts[2],  r, ba[2]-halfAngle, ba[2]+halfAngle, **self.opts_k),
+        Wedge(     tpts[3],  r, ba[3]-halfAngle, ba[3]+halfAngle, **self.opts_w),
+        Wedge(     tpts[4],  r, ba[4]-halfAngle, ba[4]+halfAngle, **self.opts_k),
+        Wedge(     tpts[5],  r, ba[5]-halfAngle, ba[5]+halfAngle, **self.opts_w),
+        Wedge(     tpts[6],  r, ba[6]-halfAngle, ba[6]+halfAngle, **self.opts_k),
+        Wedge(     tpts[7],  r, ba[7]-halfAngle, ba[7]+halfAngle, **self.opts_w),
+        Wedge(     tpts[8],  r, ba[8]-halfAngle, ba[8]+halfAngle, **self.opts_k)
+      ]
+
+    # checker board
+    else:
+
+      halfAngle = 0
+      r = 0
+
+      ba = [
+        None
+      ]
+
+      tpts = [
+        [0,0]
+      ]
+
+      template = [
+        Rectangle(tpts[0],side,side, **self.opts_k)
+      ]
+
+    # calc how much more is needed for the rotation
+    abs_angle_rad = math.radians(abs(self.angle))
+    extra_w = self.height*math.tan(abs_angle_rad) # + side
+    extra_h = self.width *math.tan(abs_angle_rad) # + side
+    # would like to pass (0,0)
+    extra_w = int(extra_w/(2*side)+1)*2*side
+    extra_h = int(extra_h/(2*side)+1)*2*side
+
+    a = np.arange(-extra_w, self.width +extra_w, 2*side)
+    b = np.arange(-extra_h, self.height+extra_h, 2*side)
+
+    for x, y in [(x,y) for x in a for y in b]:
+      self.generate_cell(x     ,y     ,tpts,template,halfAngle,r,ba)
+      self.generate_cell(x+side,y+side,tpts,template,halfAngle,r,ba)
+
+
+  # test 
+  def test(self):
+
+    x = [0, 100,   0]
+    y = [0,   0, 100]
+    self.ax.fill(x, y)
+
+    circ = Circle((0,0),0.01,color="red")
+    #circ.set_transform(t_end)
+    self.ax.add_patch(circ)
+    circ = Circle((100,0),1,color="red")
+    #circ.set_transform(t_end)
+    self.ax.add_patch(circ)
+    circ = Circle((0,100),1,color="red")
+    #circ.set_transform(t_end)
+    self.ax.add_patch(circ)
+    circ = Circle((50,50),1,color="red")
+    #circ.set_transform(t_end)
+    self.ax.add_patch(circ)
+
+  # save function
+  def save(self):
+
+    pp = PdfPages(self.pdf_name)
+    self.fig.tight_layout(pad=0)
+
+    #plt.show()
+
+    self.fig.savefig(pp,format='pdf',bbox_inches='tight',pad_inches=0)
+    #self.fig.savefig(pp,format='pdf',pad_inches=0)
+    pp.close()
+
+
+
+if __name__ == "__main__":
+
+  #ep = Escher_Pattern("test.pdf", escher=2.0, lpm=50, rotate=10)
+  #http://192.168.0.137/escher/escher_pattern.php?PAGE_WIDTH=1524&PAGE_HEIGHT=3048&LPM=2.705449885575893&ROTATE=14.036243467
+  #ep = Escher_Pattern(width= 1524, height= 3048, escher=0, lpm=2.705449885575893, rotate=10)
+  ep = Escher_Pattern(width= 1524, height= 3048, escher=2, lpm=2.705449885575893, rotate=14.036243467)
+  #ep = Escher_Pattern(width= 160, height= 320, escher=2, lpm=50, rotate=13)
+  ep.generate()
+  ep.save()