def detect_craters_with_model(model, sd_input_images, ctrs):
pred = model.predict(sd_input_images)
images_count = len(sd_input_images)
for i in range(images_count):
print(i)
labeled = get_craters_from_database(ctrs, i)
predicted = tmt.template_match_t(pred[i].copy(), minrad=2.)
def main():
# pdb.set_trace()
zenodo_path = './mars_data/'
model = load_model('models/model_30k.h5')
#### TEST CRATERS
test_imgs = h5py.File(zenodo_path + '/mars_images_5k.hdf5', 'r')
test_data = {
'imgs': [
test_imgs['input_images'][...].astype('float32'),
test_imgs['target_masks'][...].astype('float32')
]
}
proc.preprocess(test_data)
sd_input_images = test_data['imgs'][0]
sd_target_masks = test_data['imgs'][1]
images = [25, 36]
plot_dir = "plots"
for iwant in images:
pred = model.predict(sd_input_images[iwant:iwant + 1])
extracted_rings = tmt.template_match_t(
pred[0].copy(), minrad=2.) # x coord, y coord, radius
fig = plt.figure(figsize=[16, 16])
plt.rcParams["font.size"] = 20
[[ax1, ax4], [ax2, ax3]] = fig.subplots(2, 2)
ax1.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[iwant].squeeze(),
origin='upper',
cmap='Greys_r')
ax3.imshow(pred[0], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax4.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y),
r,
color='blue',
fill=False,
linewidth=2,
alpha=0.5)
ax4.add_artist(circle)
ax1.set_title('Mars DEM Image')
ax2.set_title('Ground-Truth Target Mask')
ax3.set_title('CNN Predictions')
ax4.set_title('Post-CNN Craters')
current_dir = os.path.dirname(os.path.abspath(__file__))
plot_location = os.path.join(
current_dir,
plot_dir + "/trained_model_results" + str(iwant) + ".png")
plt.savefig(plot_location)
def extract_unique_craters(CP, craters_unique):
"""Top level function that extracts craters from model predictions,
converts craters from pixel to real (degree, km) coordinates, and filters
out duplicate detections across images.
Parameters
----------
CP : dict
Crater Parameters needed to run the code.
craters_unique : array
Empty master array of unique crater tuples in the form
(long, lat, radius).
Returns
-------
craters_unique : array
Filled master array of unique crater tuples.
"""
# Load/generate model preds
try:
preds = h5py.File(CP['dir_preds'], 'r')[CP['datatype']]
print("Loaded model predictions successfully")
except:
print("Couldnt load model predictions, generating")
preds = get_model_preds(CP)
# need for long/lat bounds
P = h5py.File(CP['dir_data'], 'r')
llbd, pbd, distcoeff = ('longlat_bounds', 'pix_bounds',
'pix_distortion_coefficient')
#r_moon = 1737.4
dim = (float(CP['dim']), float(CP['dim']))
N_matches_tot = 0
for i in range(CP['start_of_images'],
CP['start_of_images'] + CP['n_imgs']):
id = proc.get_id(i)
coords = tmt.template_match_t(preds[i])
# convert, add to master dist
if len(coords) > 0:
new_craters_unique = estimate_longlatdiamkm(
dim, P[llbd][id], P[distcoeff][id][0], coords)
N_matches_tot += len(coords)
# Only add unique (non-duplicate) craters
if len(craters_unique) > 0:
craters_unique = add_unique_craters(new_craters_unique,
craters_unique, CP['llt2'],
CP['rt2'])
else:
craters_unique = np.concatenate(
(craters_unique, new_craters_unique))
np.save(CP['dir_result'], craters_unique)
return craters_unique
def get_matched_craters_indices_in_single_image(my_craters, model_prediction,
all_craters):
[real_coordinates, labeled_craters] = get_image_craters_data(my_craters)
predicted = tmt.template_match_t(model_prediction, minrad=2.)
[match, fn, fp] = sc.match_circle_lists(labeled_craters, predicted, 0.1)
matched_craters = [x[0] for x in match]
matched_crater_indices = []
for detected_crater in real_coordinates[matched_craters]:
crater_index_in_list = get_index_of_detected_crater_in_the_list(
all_craters, detected_crater)
matched_crater_indices.append(crater_index_in_list)
return np.array(matched_crater_indices)
def main():
# pdb.set_trace()
path = './input_data/'
model = load_model('models/model_keras1.2.2.h5')
#### TEST CRATERS
test_imgs = h5py.File(path + '/Mercury_images.hdf5', 'r')
images = test_imgs['input_images'][:100, :, :].astype('float32')
test_data = {'imgs': [images[np.sum(images, axis=(1, 2)) > 0]]}
#for img in test_data['imgs'][0]:
# print(np.sum(img), img[img > 0].shape)
proc.preprocess(test_data)
sd_input_images = test_data['imgs'][0]
print(len(sd_input_images))
images = [2, 10, 20, 44]
plot_dir = "plots"
for iwant in images:
print("Predicting on image", iwant)
pred = model.predict(sd_input_images[iwant:iwant + 1])
extracted_rings = tmt.template_match_t(
pred[0].copy(), minrad=2.) # x coord, y coord, radius
fig = plt.figure(figsize=[9, 9])
[ax1, ax2, ax3] = fig.subplots(1, 3)
ax1.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(pred[0], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax3.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y),
r,
color='blue',
fill=False,
linewidth=2,
alpha=0.5)
ax3.add_artist(circle)
ax1.set_title('Mercury DEM Image')
ax2.set_title('CNN Predictions')
ax3.set_title('Post-CNN Craters')
current_dir = os.path.dirname(os.path.abspath(__file__))
plot_location = os.path.join(
current_dir,
plot_dir + "/trained_model_results_Mercury" + str(iwant) + ".png")
plt.savefig(plot_location)
def extract_unique_craters(CP, craters_unique):
"""Top level function that extracts craters from model predictions,
converts craters from pixel to real (degree, km) coordinates, and filters
out duplicate detections across images.
Parameters
----------
CP : dict
Crater Parameters needed to run the code.
craters_unique : array
Empty master array of unique crater tuples in the form
(long, lat, radius).
Returns
-------
craters_unique : array
Filled master array of unique crater tuples.
"""
# Load/generate model preds
try:
preds = h5py.File(CP['dir_preds'], 'r')[CP['datatype']]
print("Loaded model predictions successfully")
except:
print("Couldnt load model predictions, generating")
preds = get_model_preds(CP)
# need for long/lat bounds
P = h5py.File(CP['dir_data'], 'r')
llbd, pbd, distcoeff = ('longlat_bounds', 'pix_bounds',
'pix_distortion_coefficient')
#r_moon = 1737.4
dim = (float(CP['dim']), float(CP['dim']))
N_matches_tot = 0
for i in range(CP['start_of_images'],CP['start_of_images']+CP['n_imgs']):
id = proc.get_id(i)
coords = tmt.template_match_t(preds[i])
%f""" % np.max(maxrad))
print("")
def keys(f):
return [key for key in f.keys()]
'''
--------------------------------------------------------------------------------------
'''
preds , data = get_model_preds(CP)
for i in range (1,20):
img_no=i
#Use scikit-image template matching to extract crater locations. Only search for craters with r >= 3 pixels.
extracted_rings = tmt.template_match_t(preds[img_no].copy(), minrad=1.)
train_imgs = h5py.File('/home/karan/deepmars/input_data/train_images.hdf5', 'r')
crater=pd.HDFStore('/home/karan/deepmars/input_data/train_craters.hdf5', 'r')
fig = plt.figure(figsize=[16, 16])
[[ax1, ax2], [ax3, ax4]] = fig.subplots(2,2)
ax1.imshow(train_imgs['input_images'][img_no][...], origin='upper', cmap='Greys_r', vmin=50, vmax=200)
ax2.imshow(train_imgs['target_masks'][img_no][...], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax3.imshow(preds[img_no], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax4.imshow(train_imgs['input_images'][img_no][...], origin='upper', cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y), r, color='blue', fill=False, linewidth=2, alpha=0.5)
ax4.add_artist(circle)
ax1.set_title('Venus DEM Image')
def extract_unique_craters(CP, craters_unique):
"""Top level function that extracts craters from model predictions,
converts craters from pixel to real (degree, km) coordinates, and filters
out duplicate detections across images.
Parameters
----------
CP : dict
Crater Parameters needed to run the code.
craters_unique : array
Empty master array of unique crater tuples in the form
(long, lat, radius).
Returns
-------
craters_unique : array
Filled master array of unique crater tuples.
"""
# Load/generate model preds
try:
preds = h5py.File(CP['dir_preds'], 'r')[CP['datatype']]
print("Loaded model predictions successfully")
except:
print("Couldnt load model predictions, generating")
preds = get_model_preds(CP)
Data, Carters = get_data(CP)
# need for long/lat bounds
P = h5py.File(CP['dir_data'], 'r')
llbd, pbd, distcoeff = ('longlat_bounds', 'pix_bounds',
'pix_distortion_coefficient')
#r_moon = 1737.4
dim = (float(CP['dim']), float(CP['dim']))
N_matches_tot = 0
if not os.path.exists(CP['result_img']):
os.mkdir(CP['result_img'])
lenstr = ""
lenstr1 = "true_carter"
lenstr2 = "detect_carter"
lenstr3 = "undetected_carter"
num = 0
num1 = 0
num2 = 0
num3 = 0
for i in range(CP['n_imgs']):
id = proc.get_id(i, 2)
print("Drawing picture:%d" % i)
input_images = Data[CP['datatype']][0][i]
imgs = Image.fromarray(input_images.astype('uint8')).convert('RGB')
img = cv2.cvtColor(np.asarray(imgs), cv2.COLOR_RGB2BGR)
coords = tmt.template_match_t(preds[i])
num = num + len(coords)
lenstr = lenstr + " " + str(len(coords))
matplotlib.image.imsave(CP['result_img'] + "/" + str(i) + '_mask.jpg',
preds[i])
true_carter, detect_carter, Undetected_carter = get_coords_classification(
coords, Carters[i])
lenstr1 = lenstr1 + " " + str(len(true_carter))
num1 = num1 + len(true_carter)
lenstr2 = lenstr2 + " " + str(len(detect_carter))
num2 = num2 + len(detect_carter)
lenstr3 = lenstr3 + " " + str(len(Undetected_carter))
num3 = num3 + len(Undetected_carter)
draw_pic(img, coords, Carters[i],
CP['result_img'] + "/" + str(i) + '.jpg')
if len(coords) > 0:
# for i in range(len(coords)):
new_craters_unique = estimate_longlatdiamkm(
dim, P[llbd][id], P[distcoeff][id][0], coords)
N_matches_tot += len(coords)
#print(id,new_craters_unique)
# Only add unique (non-duplicate) craters
if len(craters_unique) > 0:
craters_unique = add_unique_craters(new_craters_unique,
craters_unique, CP['llt2'],
CP['rt2'])
else:
craters_unique = np.concatenate(
(craters_unique, new_craters_unique))
print(lenstr)
print("total num:%d" % num)
print(lenstr1)
print(num1)
print(lenstr2)
print(num2)
print(lenstr3)
print(num3)
np.save(CP['dir_result'], craters_unique)
return craters_unique
def main():
pdb.set_trace()
zenodo_path = './data/'
deepmoon_path = os.path.dirname(os.getcwd())
train_imgs = h5py.File(zenodo_path + 'train_images.hdf5', 'r')
fig = plt.figure(figsize=[12, 6])
[ax1, ax2] = fig.subplots(1, 2)
ax1.imshow(train_imgs['input_images'][3][...],
origin='upper',
cmap='Greys_r',
vmin=120,
vmax=200)
ax2.imshow(train_imgs['target_masks'][3][...],
origin='upper',
cmap='Greys_r')
plt.show()
ctrs = pd.HDFStore(zenodo_path + 'train_craters.hdf5', 'r')
# pdb.set_trace()
Image.MAX_IMAGE_PIXELS = None
img = Image.open(zenodo_path +
"/LunarLROLrocKaguya_118mperpix.png").convert("L")
# Read and combine the LROC and Head datasets (stored under ../catalogues)
craters = igen.ReadLROCHeadCombinedCraterCSV(
filelroc="catalogues/LROCCraters.csv",
filehead="catalogues/HeadCraters.csv")
# Generate 100 image/target sets, and corresponding crater dataframes. np.random.seed is set for consistency.
igen.GenDataset(img,
craters,
zenodo_path + '/test_zenodo',
amt=25,
seed=1337)
gen_imgs = h5py.File(zenodo_path + '/test_zenodo_images.hdf5', 'r')
sample_data = {
'imgs': [
gen_imgs['input_images'][...].astype('float32'),
gen_imgs['target_masks'][...].astype('float32')
]
}
proc.preprocess(
sample_data
) #now, input images is shape 25 x 256 x 256 x 1, target_masks is shape 25 x 256 x 256
sd_input_images = sample_data['imgs'][0] #25 x 256 x 256 x 1
sd_target_masks = sample_data['imgs'][1] #25 x 256 x 256p
# Plot the data for fun.
fig = plt.figure(figsize=[12, 6])
[ax1, ax2] = fig.subplots(1, 2)
ax1.imshow(sd_input_images[5].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[5].squeeze(), origin='upper', cmap='Greys_r')
plt.savefig("plots/processed_image_and_mask1.png")
fig = plt.figure(figsize=[12, 6])
[ax1, ax2] = fig.subplots(1, 2)
ax1.imshow(sd_input_images[8].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[8].squeeze(), origin='upper', cmap='Greys_r')
plt.savefig("plots/processed_image_and_mask2.png")
fig = plt.figure(figsize=[12, 6])
[ax1, ax2] = fig.subplots(1, 2)
ax1.imshow(sd_input_images[12].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[12].squeeze(), origin='upper', cmap='Greys_r')
plt.savefig("plots/processed_image_and_mask3.png")
fig = plt.figure(figsize=[12, 6])
[ax1, ax2] = fig.subplots(1, 2)
ax1.imshow(sd_input_images[16].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[16].squeeze(), origin='upper', cmap='Greys_r')
plt.savefig("plots/processed_image_and_mask4.png")
sample_images = train_imgs['input_images'][0:20]
sample_masks = train_imgs['target_masks'][0:20]
pdb.set_trace()
model = load_model('models/model_30k.h5')
#### TEST CRATERS
test_imgs = h5py.File(zenodo_path + '/test_images.hdf5', 'r')
test_data = {
'imgs': [
test_imgs['input_images'][...].astype('float32'),
test_imgs['target_masks'][...].astype('float32')
]
}
proc.preprocess(test_data)
sd_input_images = test_data['imgs'][0]
sd_target_masks = test_data['imgs'][1]
iwant = 3
pred = model.predict(sd_input_images[iwant:iwant + 1])
extracted_rings = tmt.template_match_t(
pred[0].copy(), minrad=2.) # x coord, y coord, radius
fig = plt.figure(figsize=[16, 16])
[[ax1, ax2], [ax3, ax4]] = fig.subplots(2, 2)
ax1.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[iwant].squeeze(),
origin='upper',
cmap='Greys_r')
ax3.imshow(pred[0], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax4.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y),
r,
color='blue',
fill=False,
linewidth=2,
alpha=0.5)
ax4.add_artist(circle)
ax1.set_title('Moon DEM Image')
ax2.set_title('Ground-Truth Target Mask')
ax3.set_title('CNN Predictions')
ax4.set_title('Post-CNN Craters')
plt.savefig("plots/trained_model_results1.png")
iwant = 6
pred = model.predict(sd_input_images[iwant:iwant + 1])
extracted_rings = tmt.template_match_t(
pred[0].copy(), minrad=2.) # x coord, y coord, radius
fig = plt.figure(figsize=[16, 16])
[[ax1, ax2], [ax3, ax4]] = fig.subplots(2, 2)
ax1.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[iwant].squeeze(),
origin='upper',
cmap='Greys_r')
ax3.imshow(pred[0], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax4.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y),
r,
color='blue',
fill=False,
linewidth=2,
alpha=0.5)
ax4.add_artist(circle)
ax1.set_title('Moon DEM Image')
ax2.set_title('Ground-Truth Target Mask')
ax3.set_title('CNN Predictions')
ax4.set_title('Post-CNN Craters')
plt.savefig("plots/trained_model_results2.png")
iwant = 13
pred = model.predict(sd_input_images[iwant:iwant + 1])
extracted_rings = tmt.template_match_t(
pred[0].copy(), minrad=2.) # x coord, y coord, radius
fig = plt.figure(figsize=[16, 16])
[[ax1, ax2], [ax3, ax4]] = fig.subplots(2, 2)
ax1.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap='Greys_r',
vmin=0,
vmax=1.1)
ax2.imshow(sd_target_masks[iwant].squeeze(),
origin='upper',
cmap='Greys_r')
ax3.imshow(pred[0], origin='upper', cmap='Greys_r', vmin=0, vmax=1)
ax4.imshow(sd_input_images[iwant].squeeze(),
origin='upper',
cmap="Greys_r")
for x, y, r in extracted_rings:
circle = plt.Circle((x, y),
r,
color='blue',
fill=False,
linewidth=2,
alpha=0.5)
ax4.add_artist(circle)
ax1.set_title('Moon DEM Image')
ax2.set_title('Ground-Truth Target Mask')
ax3.set_title('CNN Predictions')
ax4.set_title('Post-CNN Craters')
plt.savefig("plots/trained_model_results3.png")