Stereo and thermal update

crop/stereo.py

@@ -67,7 +67,7 @@ def bin_to_png(in_dirs, out_dirs, plot_dir, convt):
             fail("\tFailed to process folder %s: %s" % (i, str(ex)))
 
 def fail(reason):
-    print(reason)
+    print (reason)
 
 def lower_keys(in_dict):
     if type(in_dict) is dict:
@@ -539,6 +539,12 @@ def stitch_plot_rgb_image(in_dir, out_dir, str_date, convt):
     img_hts = int(round((plot_bounds[1]-plot_bounds[0])/field_dist_per_pix))+2000
     stitched_img = np.zeros((img_hts,img_wids,3),np.uint8)
 
+    rect_x_min = img_wids
+    rect_y_min = img_hts
+    rect_x_max = 0
+    rect_y_max = 0
+
+
     start_offset = 500
     for json_file in metas:
         json_path = os.path.join(in_dir, json_file)
@@ -557,23 +563,34 @@ def stitch_plot_rgb_image(in_dir, out_dir, str_date, convt):
             print(1)
             continue
 
+        if x_start < rect_x_min :
+            rect_x_min = x_start
+        if y_start < rect_y_min:
+            rect_y_min = y_start
+        if x_start+width > rect_x_max:
+            rect_x_max = x_start+width
+        if y_start+height > rect_y_max:
+            rect_y_max = y_start+height
+
         stitched_img[y_start:y_start+height, x_start:x_start+width] = img
 
+    save_img = stitched_img[rect_y_min:rect_y_max, rect_x_min:rect_x_max]
+
     # save output
     out_file_name = '{}_{}.png'.format(str_date, dir_name)
-    cv2.imwrite(os.path.join(out_dir, out_file_name), stitched_img)
+    cv2.imwrite(os.path.join(out_dir, out_file_name), save_img)
 
     return
 
 def test():
 
-    str_date = '2017-05-24'
+    str_date = '2019-06-18'
 
     in_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/stereoTop/', str_date)
     out_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/StitchedPlotRGB', str_date)
 
     convt = terra_common.CoordinateConverter()
-    qFlag = convt.bety_query(str_date, False)
+    qFlag = convt.bety_query(str_date)
 
     if not os.path.isdir(out_dir):
         os.makedirs(out_dir)
@@ -601,24 +618,21 @@ def test_single_dir():
     str_date = '2018-05-24'
 
     convt = terra_common.CoordinateConverter()
-    qFlag = convt.bety_query(str_date, False)
+    qFlag = convt.bety_query(str_date)
 
     stitch_plot_rgb_image(in_dir, out_dir, str_date, convt)
 
     stitch_plot_rgb_image('/media/zli/Elements/ua-mac/Level_2/RgbCropToPlot/2017-05-05/41-09-649', '/media/zli/Elements/ua-mac/Level_2/StitchedPlotRGB/2017-05-05/41-09-649', str_date, convt)
 
     return
 
-def full_season_crop_rgb(raw_rgb_dir, out_dir, plot_dir, start_date, end_date):
+def full_season_crop_rgb(raw_rgb_dir, out_dir, plot_dir, start_date, end_date, convt):
 
     # initialize data structure
     d0 = datetime.strptime(start_date, '%Y-%m-%d').date()
     d1 = datetime.strptime(end_date, '%Y-%m-%d').date()
     deltaDay = d1 - d0
 
-    convt = terra_common.CoordinateConverter()
-    qFlag = convt.bety_query(start_date, False) # All plot boundaries in one season is the same
-
     # loop one season directories
     for i in range(deltaDay.days+1):
         str_date = str(d0+timedelta(days=i))
@@ -628,25 +642,81 @@ def full_season_crop_rgb(raw_rgb_dir, out_dir, plot_dir, start_date, end_date):
 
         out_path = os.path.join(out_dir, str_date)
 
+        plot_path = os.path.join(plot_dir, str_date)
+
         if not os.path.isdir(raw_path):
             continue
 
-        #crop_rgb_imageToPlot(raw_path, out_path, plot_dir, convt)
-        full_day_multi_process(raw_path, out_path, plot_dir, convt)
+        if not os.path.isdir(out_path):
+            os.mkdir(out_path)
+
+        if not os.path.isdir(plot_path):
+            os.mkdir(plot_path)
+
+        crop_rgb_imageToPlot(raw_path, out_path, plot_path, convt)
+        #full_day_multi_process(raw_path, out_path, plot_dir, convt)
 
     return
 
-def main():
-    start_date = '2017-04-15'  # S6 start date
-    end_date = '2017-08-31'   # S6 end date
+def full_season_rgb_stitch(png_dir, stitch_dir, start_date, end_date, convt):
+
+    # initialize data structure
+    d0 = datetime.strptime(start_date, '%Y-%m-%d').date()
+    d1 = datetime.strptime(end_date, '%Y-%m-%d').date()
+    deltaDay = d1 - d0
+
+    print(deltaDay.days)
+
+    # loop one season directories
+    for i in range(deltaDay.days+1):
+        str_date = str(d0+timedelta(days=i))
+        print(str_date)
+
+        png_path = os.path.join(png_dir, str_date)
+
+        stitch_path = os.path.join(stitch_dir, str_date)
+
+        if not os.path.isdir(png_path):
+            continue
+
+        if not os.path.isdir(stitch_path):
+            os.makedirs(stitch_path)
+
+        list_dirs = os.listdir(png_path)
 
-    args = options()
+        for d in list_dirs:
+            in_path = os.path.join(png_path, d)
+            out_path = os.path.join(stitch_path, d)
+
+            if not os.path.isdir(in_path):
+                continue
+
+            if not os.path.isdir(out_path):
+                os.mkdir(out_path)
+
+            stitch_plot_rgb_image(in_path, out_path, str_date, convt)
 
-    full_season_crop_rgb('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/raw_data/stereoTop',
-                          '/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_1/stereoTop',
-                           '/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/stereoTop', start_date, end_date)
-    #full_season_crop_rgb(args.in_dir, args.out_dir, args.plot_dir, start_date, end_date)
+    return
 
+def main():
+    start_date = '2018-06-02'  # S9 start date
+    end_date = '2018-06-05'   # S9 end date
+
+    convt = terra_common.CoordinateConverter()
+    qFlag = convt.bety_query('2019-06-18') # All plot boundaries in one season should be the same, currently 2019-06-18 works best
+
+    if not qFlag:
+        return
+    #args = options()
+
+    raw_dir = '/media/zli/Elements/ua-mac/raw_data/stereoTop/'
+    out_dir = '/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_1/stereoTop'
+    plot_dir = '/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/rgb_crop'
+    stitch_dir = '/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/StitchedPlotRGB'
+
+    #full_season_crop_rgb(raw_dir, out_dir, plot_dir, start_date, end_date, convt)
+
+    full_season_rgb_stitch(plot_dir, stitch_dir, start_date, end_date, convt)
 
 
 if __name__ == '__main__':
@@ -661,4 +731,4 @@ def main():
 
 
 
-
+

crop/thermalCropping.py

@@ -4,7 +4,7 @@
 @author: zli
 '''
 
-import sys, os.path, json, random, terra_common, math
+import sys, os.path, json, random, terra_common, math, argparse
 import matplotlib.pyplot as plt
 from matplotlib import cm
 from glob import glob
@@ -13,7 +13,7 @@
 from numpy.matlib import repmat
 from scipy.ndimage.filters import convolve
 from PIL import Image
-from datetime import date, timedelta
+from datetime import date, timedelta, datetime
 import shutil
 import cv2
 
@@ -424,7 +424,7 @@ def find_input_files(in_dir):
 
 
 def fail(reason):
-    print >> sys.stderr, reason
+    print (sys.stderr, reason)
 
 def extract_roiBox_from_metadata(metadata):
 
@@ -466,6 +466,11 @@ def stitch_plot_thermal_image(in_dir, out_dir, str_date, convt):
     img_hts = int(round((plot_bounds[1]-plot_bounds[0])/field_dist_per_pix))+800
     stitched_img = np.zeros((img_hts,img_wids,3),np.uint8)
 
+    rect_x_min = img_wids
+    rect_y_min = img_hts
+    rect_x_max = 0
+    rect_y_max = 0
+
     start_offset = 500
     for json_file in metas:
         json_path = os.path.join(in_dir, json_file)
@@ -484,22 +489,135 @@ def stitch_plot_thermal_image(in_dir, out_dir, str_date, convt):
             print(1)
             continue
 
+        if x_start < rect_x_min :
+            rect_x_min = x_start
+        if y_start < rect_y_min:
+            rect_y_min = y_start
+        if x_start+width > rect_x_max:
+            rect_x_max = x_start+width
+        if y_start+height > rect_y_max:
+            rect_y_max = y_start+height
+
         stitched_img[y_start:y_start+height, x_start:x_start+width] = img
 
+    save_img = stitched_img[rect_y_min:rect_y_max, rect_x_min:rect_x_max]
     # save output
     out_file_name = '{}_{}.png'.format(str_date, dir_name)
-    cv2.imwrite(os.path.join(out_dir, out_file_name), stitched_img)
+    cv2.imwrite(os.path.join(out_dir, out_file_name), save_img)
 
     return
+
+def full_season_thermalCrop_frame(in_dir, out_dir, plot_dir, png_dir, start_date, end_date, convt):
 
-def main(convt, str_date):
+    # initialize data structure
+    d0 = datetime.strptime(start_date, '%Y-%m-%d').date()
+    d1 = datetime.strptime(end_date, '%Y-%m-%d').date()
+    deltaDay = d1 - d0
+
+    print(deltaDay.days)
+
+    # loop one season directories
+    for i in range(deltaDay.days+1):
+        str_date = str(d0+timedelta(days=i))
+        print(str_date)
+
+        raw_path = os.path.join(in_dir, str_date)
+
+        out_path = os.path.join(out_dir, str_date)
+
+        plot_path = os.path.join(plot_dir, str_date)
+
+        png_path = os.path.join(png_dir, str_date)
+
+        if not os.path.isdir(raw_path):
+            continue
+
+        if not os.path.isdir(out_path):
+            os.makedirs(out_path)
+
+        if not os.path.isdir(plot_path):
+            os.makedirs(plot_path)
+
+        if not os.path.isdir(png_path):
+            os.makedirs(png_path)
+
+        #crop_rgb_imageToPlot(raw_path, out_path, plot_dir, convt)
+        crop_thermal_imageToPlot(raw_path, out_path, plot_path, png_path, convt)
+        #full_day_gen_cc(raw_path, out_path, convt)
+
+    return
+
+
 
+def full_season_thermal_stitch(png_dir, stitch_dir, start_date, end_date, convt):
+
+    # initialize data structure
+    d0 = datetime.strptime(start_date, '%Y-%m-%d').date()
+    d1 = datetime.strptime(end_date, '%Y-%m-%d').date()
+    deltaDay = d1 - d0
+
+    print(deltaDay.days)
+
+    # loop one season directories
+    for i in range(deltaDay.days+1):
+        str_date = str(d0+timedelta(days=i))
+        print(str_date)
+
+        png_path = os.path.join(png_dir, str_date)
+
+        stitch_path = os.path.join(stitch_dir, str_date)
+
+        if not os.path.isdir(png_path):
+            continue
+
+        if not os.path.isdir(stitch_path):
+            os.makedirs(stitch_path)
+
+        list_dirs = os.listdir(png_path)
+
+        for d in list_dirs:
+            in_path = os.path.join(png_path, d)
+            out_path = os.path.join(stitch_path, d)
+
+            if not os.path.isdir(in_path):
+                continue
+
+            if not os.path.isdir(out_path):
+                os.mkdir(out_path)
+
+            stitch_plot_thermal_image(in_path, out_path, str_date, convt)
+
+    return
+
+def main():
 
+    '''
     in_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/raw_data/flirlrCamera', str_date)
     out_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_1/thermalData', str_date)
     plot_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/thermalCropToPlot/', str_date)
     png_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/thermalCropToPlot_png/', str_date)
     crop_thermal_imageToPlot(in_dir, out_dir, plot_dir, png_dir, convt)
+    '''
+    print("start...")
+
+    start_date = '2018-06-02'
+    end_date = '2018-06-08'
+
+    convt = terra_common.CoordinateConverter()
+    qFlag = convt.bety_query('2019-06-18') # All plot boundaries in one season should be the same, currently 2019-06-18 works best
+
+    if not qFlag:
+        return
+
+    in_dir = os.path.join('/media/zli/Elements/ua-mac/raw_data/flirlrCamera')
+    out_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_1/thermalData')
+    plot_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/thermalCropToPlot/')
+    png_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/thermalCropToPlot_png/')
+    stitch_dir = os.path.join('/media/zli/Seagate Backup Plus Drive/OPEN/ua-mac/Level_2/StitchedPlotThermal')
+
+    #full_season_thermalCrop_frame(in_dir, out_dir, plot_dir, png_dir, start_date, end_date, convt)
+
+    full_season_thermal_stitch(png_dir, stitch_dir, start_date, end_date, convt)
 
     return
 
@@ -534,12 +652,8 @@ def test(convt, str_date):
 
 if __name__ == '__main__':
 
-    str_date = '2018-05-24'
-    convt = terra_common.CoordinateConverter()
-    convt.bety_query(str_date, False)
-
-    #main(convt, str_date)
-    test(convt, str_date)
+    main()
+    #test(convt, str_date)