def save_model_metadata(model, current_date_time):
create_directory('models/{}/models_{}/metadata'.format(
object_type, current_date_time),
format=False)
metadata = dict()
metadata['project'] = dict()
metadata['project']['type'] = os.getenv('PROJECT_TYPE').lower()
metadata['project']['object_type'] = object_type
metadata['project']['date_time'] = current_date_time
metadata['models'] = dict()
model_files = get_subfiles('models/{}/models_{}'.format(
object_type, current_date_time))
for model_name in model_files:
epoch = int(model_name.split('.')[1].split('_')[1].split('-')[0])
metadata['models'][str(epoch)] = model_name
# save model config in json format
model_config_path = save_model_config(model, current_date_time)
metadata['config'] = dict()
metadata['config']['model'] = model_config_path
metadata['config']['data_preparation'] = dict()
metadata['config']['data_preparation']['source_data'] = os.getenv(
'SATELLITE_IMAGE_PATH')
metadata['config']['data_preparation']['tilesize'] = int(
os.getenv('TILESIZE'))
metadata['config']['data_preparation']['step'] = int(os.getenv('STEP'))
metadata['config']['data_preparation']['width'] = int(os.getenv('WIDTH'))
metadata['config']['data_preparation']['height'] = int(os.getenv('HEIGHT'))
metadata['config']['data_preparation']['percent_image_with_no_annotations'] = \
float(os.getenv('PERCENT_IMAGE_WITH_NO_ANNOTATIONS'))
metadata['config']['data_preparation']['min_annotations_per_image'] = int(
os.getenv('MIN_ANNOTATIONS_PER_IMAGE'))
metadata['config']['data_preprocessing'] = dict()
metadata['config']['data_preprocessing']['percent_valid'] = float(
os.getenv('PERCENTVALID'))
metadata['config']['data_preprocessing']['percent_test'] = float(
os.getenv('PERCENTTEST'))
metadata['config']['train'] = dict()
metadata['config']['train']['epochs'] = int(os.getenv('EPOCHS'))
metadata['config']['train']['train_datasetsize'] = int(
os.getenv('TRAIN_DATASETSIZE'))
metadata['config']['train']['valid_datasetsize'] = int(
os.getenv('VALID_DATASETSIZE'))
metadata['config']['train']['batchsize'] = int(os.getenv('BATCHSIZE'))
with open(
'models/{}/models_{}/metadata/metadata_{}.json'.format(
object_type, current_date_time, current_date_time), 'w') as f:
json.dump(metadata, f)
def clone_kw_repo(root, question, attrib_value, tag):
""" This function clones the keyword repository if the user wants
individual drivers of that repository. Otherwise, it just sets the
attribute "all_drivers" of that repository tag as 'yes'
:Arguments:
1. root (xml.etree.ElementTree.Element) = parent node of the current tag
from data.xml
2. question (xml.etree.ElementTree.Element) = question tag nested under
the current tag from data.xml
3. attrib_value (str) = url of the repository in question
4. tag (xml.etree.ElementTree.Element) = current tag to which the
repository tags would be appended.
:Returns:
1. attrib_value (str) = valid url
"""
aff_pattern = re.compile("^(|y|yes)$", re.IGNORECASE)
neg_pattern = re.compile("^(n|no)$", re.IGNORECASE)
if not check_url_is_a_valid_repo(attrib_value):
attrib_value = raw_input("Please enter a valid url: ")
attrib_value = clone_kw_repo(root, question, attrib_value, tag)
else:
if root.tag == "drivers":
name = get_repository_name(attrib_value)
answer = raw_input("Do you want to clone all the drivers? "
"(yes[Enter]/no): ")
answer = transform_response(answer)
tag.set("all_drivers", answer)
if neg_pattern.match(answer):
current_dir = os.path.dirname(os.path.realpath(__file__))
path = os.path.join(current_dir, "temp")
create_dir(path)
os.chdir(path)
subprocess.call(["git", "clone", attrib_value])
os.chdir(current_dir)
temp, _ = get_subfiles(
os.path.join(path, name, 'ProductDrivers'))
drivers = get_driver_list(temp)
for i in range(1, len(drivers), 2):
print drivers[i - 1] + ". " + drivers[i]
driver_numbers = get_corresponding_numbers()
add_drivers_to_tags(tag, drivers, driver_numbers)
shutil.rmtree(path, onerror=delete_read_only)
elif not aff_pattern.match(answer):
print "The command was not recognized. Please answer yes or no."
attrib_value = clone_kw_repo(root, question, attrib_value, tag)
return attrib_value
def test_generator(test_path,
target_size=(256, 256),
flag_multi_class=False,
as_gray=False):
test_images_filename = get_subfiles(test_path)
for i in range(len(test_images_filename)):
img = io.imread(os.path.join(test_path, test_images_filename[i]))
img = img[:, :, :3]
if as_gray:
img = rgb2gray(img)
img = trans.resize(img, target_size)
# img = np.reshape(img, img.shape+(1,)) if (not flag_multi_class) else img
img = np.reshape(img, (1, ) + img.shape)
yield img
def test():
create_directories()
# prepare test data
if os.getenv('PREPARE_TEST_DATA_FLAG').upper() == 'TRUE':
prepare_data()
# get predictions
if os.getenv('GET_PREDICTIONS_FLAG').upper() == 'TRUE':
get_predictions()
# get geo-coordinates
if os.getenv('GEOREFERENCE_FLAG').upper() == 'TRUE':
files = get_subfiles(prediction_images_path)
all_geo_coordinates = Pool().map(get_individual_results, files)
all_geo_coordinates = [
point for object_geo_coordinates in all_geo_coordinates
for point in object_geo_coordinates
]
MapIntegration().combine_all_tower_geocoordinates(
os.path.join(save_results_root_path, save_csv_files_path))
print('\nSaved combine_all_tower_geocoordinates.csv successfully ...')
# save all object locations as shaepfile
print('\nPreparing Object Shapefile ...')
save_object_shapefile_path = os.path.join(
os.path.join(save_results_root_path, save_shapefiles_path))
map_integration_object = MapIntegration()
map_integration_object.save_object_locations_shapefile(
all_geo_coordinates, save_object_shapefile_path)
print('\nObject Shapefile saved successfully ...')
# Get ndvi analysis for each detected object
if os.getenv('ANALYZE_NDVI').upper() == 'TRUE':
ndvi_analysis_object = NdviAnalysis(satellite_image_ms_path,
save_object_shapefile_path,
int(os.getenv('NDVI_RADIUS')),
int(os.getenv('SIZE_X')),
int(os.getenv('SIZE_Y')))
save_ndvi_shapefile_path = os.path.join(save_results_root_path,
save_shapefiles_path)
ndvi_analysis_object.encroachment_analysis(save_ndvi_shapefile_path)
def get_predictions():
create_directory(os.getenv('PREDICTION_IMAGES_PATH'))
# get all test files
test_filenames = get_subfiles(os.getenv('TEST_IMAGES_PATH'))
# test_filenames = test_filenames[:1000]
# get test data generator
testgen = test_generator(os.getenv('TEST_IMAGES_PATH'))
test_batch_size = len(test_filenames)
# start testing
model = get_model()
print('\nStarting testing ...')
print('Using model - {}'.format(weight_file_path))
results = model.predict_generator(testgen, test_batch_size, verbose=1)
print('DONE !')
# save predictions
save_predictions(results, test_filenames)
def prepare_data():
test_files = get_subfiles(test_image_path)
# prepare test data
for test_file in test_files:
src_file = gdal.Open(os.path.join(test_image_path, test_file),
gdal.GA_ReadOnly)
width = src_file.RasterXSize
height = src_file.RasterYSize
counter = 1
for i in range(0, width, tilesize):
for j in range(0, height, tilesize):
if (i + tilesize) < width and (j + tilesize) < height:
sub_region = src_file.ReadAsArray(i, j, tilesize, tilesize)
elif (i + tilesize) < width and (j + tilesize) >= height:
sub_region = src_file.ReadAsArray(i, j, tilesize,
height - j - 1)
elif (i + tilesize) >= width and (j + tilesize) < height:
sub_region = src_file.ReadAsArray(i, j, width - i - 1,
tilesize)
else:
sub_region = src_file.ReadAsArray(i, j, width - i - 1,
height - i - 1)
filename = test_file.split('.')[0] + '_' + str(i) + '_' + str(
j)
# crop satellite image when labels are found and every time count_image_with_annot reaches
# count_image_with_annot_max
print('\ncounter: {}'.format(counter))
print('Filename: {}'.format(filename))
gdaltranString = "gdal_translate -of GTIFF -srcwin " + str(i) + ", " + str(j) + ", " + str(tilesize) \
+ ", " + str(tilesize) + " " + os.path.join(test_image_path, test_file) + " " + \
cropped_tiff_images_path + "/" + filename + ".tif"
os.system(gdaltranString)
# convert cropped tiff images to png and save to master directory
print('\nConverting tiff to png ...')
convert_all_to_png(cropped_tiff_images_path, cropped_png_images_path)
print('DONE !')
def combine_all_tower_geocoordinates(self, path):
with open(os.path.join(os.getenv('SAVE_RESULTS_ROOT_PATH'), 'towers_locations_combined.csv'), 'w', newline='') as f:
files = get_subfiles(path)
csv_writer = csv.writer(f, delimiter=',')
csv_writer.writerow(['index', 'X_img', 'Y_img', 'latitude', 'longitude'])
c = 1
for filename in files:
filepath = os.path.join(path, filename)
print('file: {}'.format(filename))
dx = int(filename.split('.')[0].split('_')[1])
dy = int(filename.split('.')[0].split('_')[2])
with open(filepath, 'r') as fd:
csv_reader = csv.reader(fd, delimiter=',')
for row in csv_reader:
if row[0].lower().strip() == 'index':
continue
csv_writer.writerow([row[0], str(int(row[1])+dx), str(int(row[2])+dy), str(row[3]), str(row[4])])
fd.close()
c += 1
f.close()
print('\nN files: {}'.format(c))
def sort_by_string(current_path, string, base_dir):
# Sort all files in the corresponding directory
subdirs = utils.get_subdirs(current_path)
subfiles = utils.get_subfiles(current_path)
for i in range(len(subfiles)):
subfiles[i] = subfiles[i].lower()
for j in range(len(subdirs)):
subdirs[j] = subdirs[j].lower()
# If directory doesn't exist, create it
if True in [string in subfile for subfile in subfiles
] and True not in [string in subdir for subdir in dir_path]:
os.makedirs(dir_path + "\\" + string, exist_ok=True)
subdirs.append(string)
base_dir.append(string)
# Move file to corresponding directory depending on a key in the file name
while True in [string in subfile for subfile in subfiles]:
os.replace(
current_path + "\\" +
str([subfile for subfile in subfiles if string in subfile][0]),
dir_path + "\\" + string + "\\" +
str([subfile for subfile in subfiles if string in subfile][0]))
subfiles.remove(
str([subfile for subfile in subfiles if string in subfile][0]))
# Recursivity stop condition
if len(subdirs) == 0 and len(subfiles) == 0:
pass
# Look for files in all directories and subdirectories
else:
for i in subdirs:
sort_by_string(current_path + "\\" + i, string, base_dir)
def prepare_master_data(label_ids=None):
# create directories
print(os.path.join(os.path.join(dataset_path, 'master')), 'images')
create_directory(
os.path.join(os.path.join(dataset_path, 'master'), 'images'))
create_directory(
os.path.join(os.path.join(dataset_path, 'master'), 'masks'))
if label_ids is None:
label_ids = []
label2images = read_label2images(source_metadata_path)
image_ids = get_image_ids(label_ids, label2images)
all_image_files = get_subfiles(os.path.join(source_data_path, 'images'))
for file in all_image_files:
base_filename = file.split('.')[0]
if base_filename in image_ids:
copyfile(
os.path.join(os.path.join(source_data_path, 'images'),
base_filename + '.jpg'),
os.path.join(
os.path.join(os.path.join(dataset_path, 'master'),
'images'), base_filename + '.jpg'))
label_image = Image.open(
os.path.join(os.path.join(source_data_path, 'labels'),
base_filename + '.png'))
label_array = np.array(label_image)
mask = np.zeros(label_array.shape)
for i in range(len(label_ids)):
res = np.where(label_array == label_ids[i])
for j in range(len(res[0])):
mask[res[0][j]][res[1][j]] = i + 1
save_mask(mask, base_filename)
print('\nMaster data prepared successfully ...\n')
def get_predictions():
create_directory(os.getenv('PREDICTION_IMAGES_PATH'))
test_filenames = get_subfiles(os.getenv('PNG_IMAGES_PATH'))
weight_file_path = os.getenv('MODELPATH')
model = unet(pretrained_weights=weight_file_path)
testgen = test_generator(os.getenv('PNG_IMAGES_PATH'))
test_batch_size = len(test_filenames)
print('\nStarting testing ...\n')
print('Using model - {}\n'.format(weight_file_path))
results = model.predict_generator(testgen, test_batch_size, verbose=1)
print('DONE !')
# save predictions - images and masks
print('\nSaving test results - masks')
save_result(os.getenv('PREDICTION_IMAGES_PATH'),
results,
test_filenames,
flag_multi_class=False,
num_class=2)
print('DONE !')
if os.getenv('SAVE_COMBINED') == 'TRUE':
create_directory(os.getenv('COMBINED_IMAGES_PATH'))
imagesdir = os.getenv('PNG_IMAGES_PATH')
masksdir = os.getenv('PREDICTION_IMAGES_PATH')
suffix = '_predict'
print('\nSaving test results - images and masks combined')
save_images_and_masks(imagesdir, masksdir, suffix, save=True)
print('DONE !')
def save_images_and_masks(imagesdir,
masksdir,
suffix='_mask',
show=False,
save=False):
all_images = get_subfiles(imagesdir)
counter = 1
for imagefilename in all_images:
filename = imagefilename.split('.')[0]
maskfilename = str(filename) + suffix + '.png'
img = cv2.imread(imagesdir + '/' + imagefilename)
mask = cv2.imread(masksdir + '/' + maskfilename)
if os.getenv('COLORMAP_FLAG').upper() == 'TRUE':
mask_modified = apply_color_map(mask)
else:
mask_modified = get_binary_image(mask)
combined_img = np.concatenate((img, mask_modified), axis=1)
if show:
cv2.imshow("annotations - Filename: {}".format(filename),
combined_img)
cv2.waitKey()
cv2.destroyAllWindows()
if save:
print('\ncounter: {}'.format(counter))
print('Filepath: {}'.format(
os.getenv('COMBINED_IMAGES_PATH') +
'/{}'.format(str(filename) + '.png'), combined_img))
cv2.imwrite(
os.getenv('COMBINED_IMAGES_PATH') +
'/{}'.format(str(filename) + '.png'), combined_img)
counter += 1
def load_nwb_from_data(dir_path):
# Get all files and directories present in the path
files = utils.get_subfiles(dir_path)
dirs = utils.get_subdirs(dir_path)
files = files + dirs
# Open YAML file with keywords, extension and keywords to exclude if existing then dump all data in a dict
if os.path.isfile(dir_path + "\\" + [subfile for subfile in files if "default" in subfile][0]):
with open(dir_path + "\\" + [subfile for subfile in files if "default" in subfile][0], 'r') as stream:
data = yaml.safe_load(stream)
# Remove the file from the list of files and directories so it isn't found twice
files.remove([subfile for subfile in files if "default" in subfile][0])
else:
data = None
home_data = dict()
# Look for another YAML file containing the keywords, extensions and keywords to exclude
for file in files:
if "yaml" not in file:
continue
# p is a placeholder until we know every yaml file name
if "subject" not in file and "ophys" not in file and "data" not in file and "p" not in file:
with open(dir_path + "\\" + file, 'r') as stream:
home_data = yaml.safe_load(stream)
# If 2 files are provided, the one given by the user will take the priority
if data is not None:
difference = set(list(data.keys())) - set(list(home_data.keys()))
for i in list(difference):
home_data[i] = data[i]
# First we create the nwb file because it will be needed for everything
converttonwb = home_data.pop("ConvertToNWB")
filtered_list = []
for i in converttonwb:
# If no extension is provided it means we are looking for a directory, so we filter the list of files and
# directory to only contain directories
if not converttonwb[i].get("extension"):
filtered_list = [file for file in files if "." not in file]
# Filter the file list depending on the extension provided in the YAML file
else:
for extension in converttonwb[i].get("extension"):
filtered_list.extend([file for file in files if extension in file])
# print("Filter result : " + str(filtered_list) + " by extension : " + str(converttonwb[i].get("extension")))
# Conditional loop to remove all files or directories not containing the keywords
# or containing excluded keywords
counter = 0
while counter < len(filtered_list):
delete = False
for keyword in converttonwb[i].get("keyword"):
if keyword not in filtered_list[counter]:
# print("Keyword not found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
for keyword_to_exclude in converttonwb[i].get("keyword_to_exclude"):
if keyword_to_exclude in filtered_list[counter]:
# print("Excluded keyword found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
counter += 1
print("Files to pass for " + i + ": " + str(filtered_list))
# If files were found respecting every element, add the whole path to pass them as arguments
yaml_path = os.path.join(dir_path, filtered_list[0])
nwb_file = test_cicada_test_paul.create_nwb_file(yaml_path)
order_list = []
if home_data.get("order"):
order_list = home_data.pop("order")
while order_list:
next_class = order_list.pop(0)
# Get classname then instantiate it
classname = getattr(test_cicada_test_paul, next_class)
converter = classname(nwb_file)
# Initialize a dict to contain the arguments to call convert
arg_dict = {}
print("Class name : " + str(next_class))
# Loop through all arguments of the convert of the corresponding class
for j in home_data[next_class]:
filtered_list = []
# If value if found it means the argument is not a file but a string/int/etc
if home_data[next_class][j].get("value") and not home_data[next_class][j].get("extension") and \
(not home_data[next_class][j].get("keyword") or not home_data[next_class][j].get("keyword_to_exclude")):
print(home_data[next_class][j].get("value")[0])
arg_dict[j] = home_data[next_class][j].get("value")[0]
else:
# If no extension is provided it means we are looking for a directory, so we filter the list of files and
# directory to only contain directories
if not home_data[next_class][j].get("extension"):
filtered_list = [file for file in files if "." not in file]
# Filter the file list depending on the extension provided in the YAML file
else:
for extension in home_data[next_class][j].get("extension"):
filtered_list.extend([file for file in files if extension in file])
# print("Filter result : " + str(filtered_list) + " by extension : " +
# str(home_data[i][j].get("extension")))
# Conditional loop to remove all files or directories not containing the keywords
# or containing excluded keywords
counter = 0
while counter < len(filtered_list):
delete = False
for keyword in home_data[next_class][j].get("keyword"):
if keyword not in filtered_list[counter]:
# print("Keyword not found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
for keyword_to_exclude in home_data[next_class][j].get("keyword_to_exclude"):
if keyword_to_exclude in filtered_list[counter]:
# print("Excluded keyword found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
counter += 1
print("Files to pass for " + j + ": " + str(filtered_list))
# If files were found respecting every element, add the whole path to pass them as arguments
if filtered_list:
arg_dict[j] = os.path.join(dir_path, filtered_list[0])
if "mat" in home_data[next_class][j].get("extension") and home_data[next_class][j].get("value"):
arg_dict[j] = [arg_dict[j]] + list(home_data[next_class][j].get("value"))
# If no file found, put the argument at None
else:
arg_dict[j] = None
# print("Arguments to pass : "******"Class name : " + str(i))
# Loop through all arguments of the convert of the corresponding class
for j in home_data[i]:
filtered_list = []
# If value if found it means the argument is not a file but a string/int/etc
if home_data[i][j].get("value") and not home_data[i][j].get("extension") and \
(not home_data[i][j].get("keyword") or not home_data[i][j].get("keyword_to_exclude")):
print(home_data[i][j].get("value")[0])
arg_dict[j] = home_data[i][j].get("value")[0]
else:
# If no extension is provided it means we are looking for a directory, so we filter the list of files and
# directory to only contain directories
if not home_data[i][j].get("extension"):
filtered_list = [file for file in files if "." not in file]
# Filter the file list depending on the extension provided in the YAML file
else:
for extension in home_data[i][j].get("extension"):
filtered_list.extend([file for file in files if extension in file])
# print("Filter result : " + str(filtered_list) + " by extension : " +
# str(home_data[i][j].get("extension")))
# Conditional loop to remove all files or directories not containing the keywords
# or containing excluded keywords
counter = 0
while counter < len(filtered_list):
delete = False
for keyword in home_data[i][j].get("keyword"):
if keyword not in filtered_list[counter]:
# print("Keyword not found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
for keyword_to_exclude in home_data[i][j].get("keyword_to_exclude"):
if keyword_to_exclude in filtered_list[counter]:
# print("Excluded keyword found in : " + str(filtered_list))
del filtered_list[counter]
# print("New list : " + str(filtered_list))
delete = True
if not delete:
counter += 1
print("Files to pass for " + j + ": " + str(filtered_list))
# If files were found respecting every element, add the whole path to pass them as arguments
if filtered_list:
arg_dict[j] = os.path.join(dir_path, filtered_list[0])
if "mat" in home_data[i][j].get("extension") and home_data[i][j].get("value"):
arg_dict[j] = [arg_dict[j]] + list(home_data[i][j].get("value"))
# If no file found, put the argument at None
else:
arg_dict[j] = None
#print("Arguments to pass : "******".nwb"
with test_cicada_test_paul.NWBHDF5IO(os.path.join(dir_path, nwb_name), 'w') as io:
io.write(nwb_file)
print("NWB file created at : " + str(os.path.join(dir_path, nwb_name)))
create = input(
"Folder does not exist, do you want to create it ? (yes/no)")
if create == "yes":
os.makedirs(sys.argv[1], exist_ok=True)
else:
exit()
print("Folder to build", sys.argv[1])
global dir_path
dir_path = sys.argv[1]
folder = os.path.basename(os.path.normpath(dir_path))
head, tail = os.path.split(os.path.normpath(dir_path))
id_dir = utils.get_subdirs(dir_path)
subfiles = utils.get_subfiles(dir_path)
for i in range(len(subfiles) - 1):
if "data" in subfiles[i]:
with open(dir_path + "\\" + subfiles[i], 'r') as stream:
data_dict = yaml.safe_load(stream)
if not data_dict.get("session_id"):
id = data_dict.get("identifier")
else:
id = data_dict.get("session_id")
stream.close()
sort_by_string(dir_path, id, id_dir)
#
# region_list = ["a000", "a001", "a002"]
# region_dir = get_subdirs(dir_path)
def train_valid_test_split(master_data_path,
train_path,
valid_path,
test_path,
percent_valid=0.2,
percent_test=0.2):
# distribute files from master to train, valid and test
all_data_filenames = get_subfiles(
os.path.join(os.path.join(dataset_path, 'master'), 'images'))
valid_filenames = random.sample(
all_data_filenames,
int((percent_valid / 100.0) * len(all_data_filenames)))
test_filenames = random.sample(
valid_filenames, int((percent_test / 100.0) * len(valid_filenames)))
train_filenames = [
x for x in all_data_filenames if x not in valid_filenames
]
valid_filenames = [x for x in valid_filenames if x not in test_filenames]
# create directories
create_directory(train_path)
create_directory(os.path.join(train_path, 'images'))
create_directory(os.path.join(train_path, 'masks'))
create_directory(test_path)
create_directory(os.path.join(test_path, 'images'))
create_directory(os.path.join(test_path, 'masks'))
create_directory(valid_path)
create_directory(os.path.join(valid_path, 'images'))
create_directory(os.path.join(valid_path, 'masks'))
# copy train files
for file in train_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(train_path, 'images'), file))
mask_filename = file.split('.')[0] + '_mask.png'
copyfile(
os.path.join(os.path.join(master_data_path, 'masks'),
mask_filename),
os.path.join(os.path.join(train_path, 'masks'), mask_filename))
print('\nTrain files copied successfully ...')
# copy validation files
for file in valid_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(valid_path, 'images'), file))
mask_filename = file.split('.')[0] + '_mask.png'
copyfile(
os.path.join(os.path.join(master_data_path, 'masks'),
mask_filename),
os.path.join(os.path.join(valid_path, 'masks'), mask_filename))
print('\nValidation files copied successfully ...')
# copy test files
for file in test_filenames:
copyfile(os.path.join(os.path.join(master_data_path, 'images'), file),
os.path.join(os.path.join(test_path, 'images'), file))
copyfile(
os.path.join(os.path.join(master_data_path, 'masks'),
mask_filename),
os.path.join(os.path.join(test_path, 'masks'), mask_filename))
print('\nTest files copied successfully ...')
def backup_packages(backup_path):
"""
Creates `packages` directory and places install list text files there.
"""
print_section_header("PACKAGES", Fore.BLUE)
mkdir_warn_overwrite(backup_path)
std_package_managers = ["brew", "brew cask", "gem"]
for mgr in std_package_managers:
# deal with package managers that have spaces in them.
print_pkg_mgr_backup(mgr)
command = "{} list".format(mgr)
dest = "{}/{}_list.txt".format(backup_path, mgr.replace(" ", "-"))
run_cmd_write_stdout(command, dest)
# cargo
print_pkg_mgr_backup("cargo")
command = "ls {}".format(home_prefix(".cargo/bin/"))
dest = "{}/cargo_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# pip
print_pkg_mgr_backup("pip")
command = "pip list --format=freeze".format(backup_path)
dest = "{}/pip_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# npm
print_pkg_mgr_backup("npm")
command = "npm ls --global --parseable=true --depth=0"
temp_file_path = "{}/npm_temp_list.txt".format(backup_path)
run_cmd_write_stdout(command, temp_file_path)
npm_dest_file = "{0}/npm_list.txt".format(backup_path)
# Parse npm output
with open(temp_file_path, mode="r+") as temp_file:
# Skip first line of file
temp_file.seek(1)
with open(npm_dest_file, mode="w+") as dest:
for line in temp_file:
dest.write(line.split("/")[-1])
os.remove(temp_file_path)
# atom package manager
print_pkg_mgr_backup("Atom")
command = "apm list --installed --bare"
dest = "{}/apm_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# sublime text 2 packages
sublime_2_path = home_prefix(
"Library/Application Support/Sublime Text 2/Packages/")
if os.path.isdir(sublime_2_path):
print_pkg_mgr_backup("Sublime Text 2")
command = ["ls", sublime_2_path]
dest = "{}/sublime2_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# sublime text 3 packages
sublime_3_path = home_prefix(
"Library/Application Support/Sublime Text 3/Installed Packages/")
if os.path.isdir(sublime_3_path):
print_pkg_mgr_backup("Sublime Text 3")
command = ["ls", sublime_3_path]
dest = "{}/sublime3_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
else:
print(sublime_3_path, "IS NOT DIR")
# macports
print_pkg_mgr_backup("macports")
command = "port installed requested"
dest = "{}/macports_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# system installs
print_pkg_mgr_backup("macOS Applications")
command = "ls /Applications/"
dest = "{}/system_apps_list.txt".format(backup_path)
run_cmd_write_stdout(command, dest)
# Clean up empty package list files
print(Fore.BLUE + "Cleaning up empty package lists..." + Style.RESET_ALL)
for file in get_subfiles(backup_path):
if os.path.getsize(file) == 0:
os.remove(file)
