updated envi file to support adding elements (like wavelength units)

David Mayerich
1 parent 2119be83
Showing 3 changed files with 67 additions and 37 deletions Show diff stats
docs/nwt_format.pptx
python/envi.py
python/muve-align.py
@@ -9,7 +9,6 @@ import os
 import numpy
 import scipy
 import matplotlib.pyplot as plt
-#import pyprind
 import sys
 from math import floor
 import progressbar
@@ -186,31 +185,62 @@ class envi_header:
  
     #save an ENVI header
     def save(self, fname):
-    	f = open(fname, "w")
-    	f.write("ENVI\n")
-    	f.write("description = {" + self.description + "}" + "\n")
-    	f.write("samples = " + str(self.samples) + "\n")
-    	f.write("lines = " + str(self.lines) + "\n")
-    	f.write("bands = " + str(self.bands) + "\n")
-    	f.write("header offset = " + str(self.header_offset) + "\n")
-    	f.write("file type = ENVI Standard" + "\n")
-    	f.write("data type = " + str(self.get_envi_type(self.type)) + "\n")
-    	f.write("interleave = " + self.interleave + "\n")
-    	f.write("sensor type = " + self.sensor_type + "\n")
-    	f.write("byte order = " + str(self.byte_order) + "\n")
-    	f.write("x start = " + str(self.x_start) + "\n")
-    	f.write("y start = " + str(self.y_start) + "\n")
-    	f.write("wavelength units = " + self.wavelength_units + "\n")
-    	f.write("z plot titles = {" + self.z_plot_titles + "}" + "\n")
+        f = open(fname, "w")
+        f.write("ENVI\n")
+        f.write("description = {" + self.description + "}" + "\n")
+        f.write("samples = " + str(self.samples) + "\n")
+        f.write("lines = " + str(self.lines) + "\n")
+        f.write("bands = " + str(self.bands) + "\n")
+        f.write("header offset = " + str(self.header_offset) + "\n")
+        f.write("file type = ENVI Standard" + "\n")
+        f.write("data type = " + str(self.get_envi_type(self.type)) + "\n")
+        f.write("interleave = " + self.interleave + "\n")
+        f.write("sensor type = " + self.sensor_type + "\n")
+        f.write("byte order = " + str(self.byte_order) + "\n")
+        f.write("x start = " + str(self.x_start) + "\n")
+        f.write("y start = " + str(self.y_start) + "\n")
+        f.write("wavelength units = " + self.wavelength_units + "\n")
+        f.write("z plot titles = {" + self.z_plot_titles + "}" + "\n")
+        
+        # save the wavelength values
+        if self.wavelength != []:
+            if len(self.wavelength) == self.bands:
+                f.write("wavelength = {")
+                f.write(",".join(map(str, self.wavelength)))
+                f.write("}\n")
+            else:
+                raise Exception("ENVI HEADER ERROR: Number of wavelengths does not match number of bands")
  
-    	f.close()
+        f.close()
  
     #sets the properties of the header to match those of the input array
-    def set(self, A):
-    	self.type = A.dtype
-    	self.samples = A.shape[2]
-    	self.lines = A.shape[1]
-    	self.bands = A.shape[0]
+    def setprops(self, A, interleave="BSQ", wavelength=[]):
+        # determine the data type automatically
+        self.type = A.dtype
+        
+        # determine the ordering based on the specified interleave
+        if interleave == "BSQ":
+            self.samples = A.shape[2]
+            self.lines = A.shape[1]
+            self.bands = A.shape[0]
+        elif interleave == "BIP":
+            self.samples = A.shape[1]
+            self.lines = A.shape[2]
+            self.bands = A.shape[0]
+        elif interleave == "BIL":
+            self.samples = A.shape[0]
+            self.lines = A.shape[2]
+            self.bands = A.shape[1]
+        else:
+            raise Exception("invalid interleave format (requires 'BSQ', 'BIP', or 'BIL') - interleave is set to {}".interleave)
+            
+        # if wavelength units are given, make sure that they match the number of bands
+        if wavelength != []:
+            if len(wavelength) != self.bands:
+                raise Exception("invalid number of wavelengths specified")
+            else:
+                self.wavelength = wavelength
+                
  
  
 class envi:
@@ -413,8 +443,8 @@ class envi:
     #read a batch of data based on the mask
     def loadbatch(self, npixels):
         i = numpy.flatnonzero(self.mask)                                      #get the indices of valid pixels
-        if len(i) == self.idx:													#if all of the pixels have been read, return an empyt array
-        	return []
+        if len(i) == self.idx:                                                    #if all of the pixels have been read, return an empyt array
+            return []
         npixels = min(npixels, len(i) - self.idx)                        #if there aren't enough pixels, change the batch size
         B = self.header.bands
  
@@ -439,14 +469,14 @@ class envi:
  
     #returns an image of the pixels that have been read using batch loading
     def batchmask(self):
-    	#allocate a new mask
-    	outmask = numpy.zeros(self.mask.shape, dtype=numpy.bool)
+        #allocate a new mask
+        outmask = numpy.zeros(self.mask.shape, dtype=numpy.bool)
  
-    	#zero out any unclassified pixels 
-    	idx = self.getidx()
-    	i = numpy.nonzero(self.mask)
-    	outmask[i[0][0:idx], i[1][0:idx]] = self.mask[i[0][0:idx], i[1][0:idx]]
-    	return outmask
+        #zero out any unclassified pixels 
+        idx = self.getidx()
+        i = numpy.nonzero(self.mask)
+        outmask[i[0][0:idx], i[1][0:idx]] = self.mask[i[0][0:idx], i[1][0:idx]]
+        return outmask
  
     def close(self):
         self.file.close()
@@ -455,11 +485,11 @@ class envi:
         self.file.close()
  
 #saves an array as an ENVI file
-def save_envi(A, fname):
+def save_envi(A, fname, interleave="BSQ", wavelength=[]):
  
     #create and save a header file
     header = envi_header();
-    header.set(A)
+    header.setprops(A, interleave, wavelength)
     header.save(fname + ".hdr")
  
     #save the raw data
@@ -96,8 +96,8 @@ def align(A, B, max_power=5):
         #warp_matrix[0, 2] = 0
     #    return warp_matrix
  
-fmask = "Z:/jack/TinkParaffinLung0.005S/*.png"
-out_dir = "Z:/jack/TinkParaffinLung0.005S/aligned"
+fmask = "D:/Dropbox/todo/lab-presentations/jack/TinkParaffinLung0.005S/*.png"
+out_dir = "D:/Dropbox/todo/lab-presentations/jack/TinkParaffinLung0.005S/aligned"
  
 if not os.path.isdir(out_dir):
     os.mkdir(out_dir)
@@ -155,4 +155,4 @@ ax.set_xlabel(&quot;Press &#39;z&#39; and &#39;x&#39; to change slices and arrow keys to align&quot;)
 plt.show()
  
 I = apply_alignment(S, warps)
-imagestack.save(I, out_dir + "/aligned_", ".bmp")
 \ No newline at end of file
+imagestack.save(I, out_dir + "/aligned_", "bmp")
 \ No newline at end of file