updated for 4-channel images and OpenCV 3

David Mayerich
1 parent 4e0db0cd
Showing 2 changed files with 56 additions and 8 deletions Show diff stats
python/imagestack.py
stim/image/image.h
@@ -2,8 +2,10 @@ import glob
 import imageio
 import numpy
 import progressbar
+import skimage.transform
+import os
  
-def loadstack(fmask, dtype=numpy.float32):
+def load(fmask, dtype=numpy.float32):
     #read the input files
     F = glob.glob(fmask)
     if(len(F)==0):
@@ -14,13 +16,16 @@ def loadstack(fmask, dtype=numpy.float32):
     I = imageio.imread(F[0])
  
     #generate the image stack
-    S = numpy.zeros((len(F), I.shape[0], I.shape[1], I.shape[2]), dtype)
+    if I.ndim == 3:
+    	S = numpy.zeros((len(F), I.shape[0], I.shape[1], I.shape[2]), dtype)
+    else:
+    	S = numpy.zeros((len(F), I.shape[0], I.shape[1]), dtype)
  
     bar = progressbar.ProgressBar(max_value=len(F))
  
     for i in range(0, len(F)):
         I = imageio.imread(F[i])
-        S[i, :, :, :] = I
+        S[i, ...] = I
         bar.update(i+1)
  
     return S
@@ -31,10 +36,35 @@ def rgb2gray(rgb):
  
     return gray
  
-def savestack(I, fname, extension = ".bmp"):
+def save(I, fname, extension = "bmp"):
     #output the final images
     bar = progressbar.ProgressBar(max_value=I.shape[0])
     #save the output files
     for i in range(0, I.shape[0]):        
-        imageio.imwrite(fname + "%03d" % i + extension, I[i, :, :, :])
-        bar.update(i+1)
 \ No newline at end of file
+        imageio.imwrite(fname + "%03d" % i + "." + extension, I[i, ...])
+        bar.update(i+1)
+
+#rescale a stack of images along X and Y by an integer value n and save to directory dest        
+def resize(fmask, dest, n, outformat=None):
+    #read the input files
+    F = glob.glob(fmask)
+    if(len(F)==0):
+        print("No image files found.")
+        return
+    
+    #initialize a progress bar
+    bar = progressbar.ProgressBar(max_value=len(F))
+    
+    #for each file
+    for i in range(0, len(F)):
+        
+        #load the file to memory
+        I = imageio.imread(F[i])
+        R = skimage.transform.downscale_local_mean(I, (n, n))
+        if outformat is None:
+            imageio.imwrite(dest+"/"+os.path.basename(F[i]), R)
+        else:
+            imageio.imwrite(dest+"/"+os.path.basename(F[i]).split('.')[0] + "." + outformat, R)
+        bar.update(i+1)
+    
+    
 \ No newline at end of file
@@ -238,7 +238,7 @@ public:
  
  
 #ifdef USING_OPENCV
-	void from_opencv(unsigned char* buffer, size_t width, size_t height) {
+	void from_opencv_888(unsigned char* buffer, size_t width, size_t height) {
 		allocate(width, height, 3);
 		T value;
 		size_t i;
@@ -252,6 +252,22 @@ public:
 			}
 		}
 	}
+	void from_opencv_8888(unsigned char* buffer, size_t width, size_t height) {
+		//std::cerr << "ERROR - this software is not yet enabled to handle RGBA images (alpha channel)." << std::endl;
+		//exit(1);
+		allocate(width, height, 4);
+		T value;
+		size_t i;
+		for (size_t c = 0; c < C(); c++) {								//copy directly
+			for (size_t y = 0; y < Y(); y++) {
+				for (size_t x = 0; x < X(); x++) {
+					i = y * X() * C() + x * C() + (3 - c);
+					value = buffer[i];
+					img[idx(x, y, c)] = value;
+				}
+			}
+		}
+	}
 #endif
 	//Copy N data points from source to dest, casting while doing so
 	template<typename S, typename D>
@@ -280,7 +296,9 @@ public:
 			type_copy<unsigned char, T>(cv_ptr, img, size());
 		//memcpy(img, cv_ptr, bytes());
 		if(C() == 3)														//if this is a 3-color image, OpenCV uses BGR interleaving
-			from_opencv(cv_ptr, X(), Y());
+			from_opencv_888(cv_ptr, X(), Y());
+		if (C() == 4)
+			from_opencv_8888(cv_ptr, X(), Y());
 #else
 		stim::filename file(filename);
 		if (file.extension() == "ppm")