def set_byte_map(class_list, raster, process, output):
"""
reclassify a map using the provided class list
Args:
class_list (list(list(int))): each list of the root list represent a byte value starting at 1.
each nested list is the value of the class that need to be included into each byte value.
raster (pathlib.Path): the path to the original image
"""
# check that the inputs are all separated
if is_overlap(class_list):
raise Exception(cm.bin.overlap)
# output for the user
output.add_live_msg(cm.bin.running)
# get the final file name
filename = Path(raster).stem
bin_map = cp.get_result_dir(process).joinpath(f'{filename}_bin_map.tif')
if bin_map.is_file():
output.add_live_msg(cm.bin.file_exist.format(bin_map), 'warning')
return bin_map
# create the bin map using the values provided by the end user
with rio.open(raster) as src:
out_meta = src.meta.copy()
out_meta.update(compress='lzw', dtype=np.uint8)
raw_data = src.read()
if class_list == []:
data = raw_data
else:
data = np.zeros_like(raw_data, dtype=np.uint8)
total_class = sum([len(c) for c in class_list])
c = 0
output.update_progress(0)
for index, class_ in enumerate(class_list):
bool_data = np.zeros_like(raw_data, dtype=np.bool_)
for val in class_:
bool_data = bool_data + (raw_data == val)
# display the advancement
c += 1
output.update_progress(c / total_class)
data_value = (bool_data * (index + 1)).astype(np.uint8)
data = data + data_value
data = data.astype(out_meta['dtype'])
with rio.open(bin_map, 'w', **out_meta) as dst:
dst.write(data)
output.add_live_msg(cm.bin.finished, 'success')
return bin_map
def run_gwb_process(process, raster, params_list, title, output, offset):
"""
run all the processes of the GWB suit according to the io
The input and output folder will be created on the fly and deleted right afterward
The result will be saved in the result_dir of the parameter component
The log will be displayed to the end user and then removed
Args:
io (GWBIo): any io inheriting from the GWBIo object
Return:
(pathlib.Path) : the path to the final .image
(pathlib.Path) : the path to the final .csv
"""
# create the tmp directories
tmp_dir = cp.get_tmp_dir()
in_dir = tmp_dir / "input"
in_dir.mkdir(exist_ok=True)
out_dir = tmp_dir / "output"
out_dir.mkdir(exist_ok=True)
# fill the tmp dir with the raster
shutil.copy(raster, in_dir)
# create the input file
parameter_file = in_dir / f"{process}-parameters.txt"
with parameter_file.open("w") as f:
star_line = ["*" * 76 + "\n"]
offset_lines = ["\n" for i in range(offset - 2)]
params_lines = [str(p) + "\n" for p in params_list]
finish_lines = ["\n"]
f.writelines(offset_lines + star_line + params_lines + star_line + finish_lines)
# create the command
command = [f"GWB_{process.upper()}", f"-i={in_dir}", f"-o={out_dir}"]
# set the argument of the process
kwargs = {
"args": command,
"cwd": Path.home(), # launch from home to avoid permissions bugs
"stdout": subprocess.PIPE,
"stderr": subprocess.PIPE,
"universal_newlines": True,
}
# start the process
output.add_live_msg(cm.gwb.start.format(process.upper()))
with subprocess.Popen(**kwargs) as p:
for line in p.stdout:
output.append_msg(line)
# file in the output directory
folder = cp.gwb[process]["folder"]
out_log = list(out_dir.glob(f"*.log"))
# if log is not there, the comutation didn't even started
# I let the display in its current state and change the color of the output to red
if len(out_log) == 0:
output.type = "error"
return []
# read the log
with open(out_log[0]) as f:
log = f.read()
output.add_live_msg(
v.Html(tag="pre", class_="info--text d-inline", children=[log])
)
# if the log file is the only file then it has crashed
try:
if folder == "":
out_files = [f for f in out_dir.glob("*.*") if not f.stem == ".log"]
else:
out_files = next(out_dir.glob(f"{raster.stem}_{folder}*/")).glob("*.*")
except:
output.add_live_msg(
v.Html(tag="pre", class_="error--text d-inline", children=[log]), "error"
)
return []
# copy the files in the result directory
files = []
for f in out_files:
final_f = shutil.copy(f, cp.get_result_dir(process))
files.append(Path(final_f))
# display the final log
output.add_live_msg(
v.Html(tag="pre", class_="success--text d-inline", children=[log]), "success"
)
return files
def run_gwb_process(process, raster, params_list, title, output, offset):
"""
run all the processes of the GWB suit according to the io
The input and output folder will be created on the fly and deleted right afterward
The result will be saved in the result_dir of the parameter component
The log will be displayed to the end user and then removed
Args:
io (GWBIo): any io inheriting from the GWBIo object
Return:
(pathlib.Path) : the path to the final .image
(pathlib.Path) : the path to the final .csv
"""
# create the tmp directories
tmp_dir = cp.get_tmp_dir()
in_dir = tmp_dir.joinpath('input')
in_dir.mkdir()
out_dir = tmp_dir.joinpath('output')
out_dir.mkdir()
# fill the tmp dir with the raster
shutil.copy(raster, in_dir)
# create the input file
parameter_file = in_dir.joinpath(f'{process}-parameters.txt')
with parameter_file.open('w') as f:
offset_lines = ['\n' for i in range(offset-1)]
params_lines = [str(p) + '\n' for p in params_list]
finish_lines = ['\n']
f.writelines(offset_lines + params_lines +finish_lines)
# create the command
command = [
f'GWB_{process.upper()}',
f'-i={in_dir}',
f'-o={out_dir}'
]
# set the argument of the process
kwargs = {
'args' : command,
'cwd' : Path('~').expanduser(), # launch from home to avoid permissions bugs
'stdout' : subprocess.PIPE,
'stderr' : subprocess.PIPE,
'universal_newlines' : True
}
# start the process
output.add_live_msg(cm.gwb.start.format(process.upper()))
with subprocess.Popen(**kwargs) as p:
for line in p.stdout:
output.append_msg(line)
# file in the output directory
folder = cp.gwb[process]["folder"]
if folder == '':
out_log = list(out_dir.glob(f'*.log'))
out_files = [f for f in out_dir.glob("*.*") if not f.stem == '.log']
else:
out_log = list(out_dir.glob(f'*.log'))
out_files = next(out_dir.glob(f'{raster.stem}_{folder}*/')).glob('*.*')
# if log is not there, the comutation didn't even started
# I let the display in its current state and change the color of the output to red
if len(out_log) == 0:
output.type = 'error'
return []
# if the log file is the only file then it has crashed
# read the log
with open(out_log[0]) as f:
log = f.read()
# copy the files in the result directory
files = []
for f in out_files:
final_f = shutil.copy(f, cp.get_result_dir(process))
files.append(Path(final_f))
# display the final log
output.add_live_msg(v.Html(tag='pre', class_='success--text d-inline', children=[log]), 'success')
return files
def set_byte_map(class_list, raster, band, process, output):
"""
reclassify a map using the provided class list
Args:
class_list (list(list(int))): each list of the root list represent a byte value starting at 1.
each nested list is the value of the class that need to be included into each byte value.
raster (pathlib.Path): the path to the original image
"""
# check that the inputs are all separated
if is_overlap(class_list):
raise Exception(cm.bin.overlap)
# output for the user
output.add_live_msg(cm.bin.running)
# get the final file name
filename = Path(raster).stem
bin_map = cp.get_result_dir(process) / f"{filename}_bin_map.tif"
if bin_map.is_file():
output.add_live_msg(cm.bin.file_exist.format(bin_map), "warning")
return bin_map
# create the bin map using the values provided by the end user
with rio.open(raster) as src:
out_meta = src.meta.copy()
out_meta.update(count=1,
compress="lzw",
dtype=np.uint8,
driver="GTiff")
with rio.open(bin_map, "w", **out_meta) as dst:
# loop on windows
# I assume windows are the same on each band
output.update_progress(0)
nb_windows = sum(1 for _ in src.block_windows(1))
for iw, block in enumerate(src.block_windows(1)):
# get the raw data on the window
window = block[1]
raw_data = src.read(band, window=window)
# reclassify data using the class_list
data = np.zeros_like(raw_data, dtype=np.uint8)
total_class = sum([len(c) for c in class_list])
for ic, class_ in enumerate(class_list):
bool_data = np.isin(raw_data, class_)
data_value = (bool_data * (ic + 1)).astype(np.uint8)
data = data + data_value
data = data.astype(out_meta["dtype"])
dst.write(data, 1, window=window)
output.update_progress((iw + 1) / nb_windows)
output.add_live_msg(cm.bin.finished, "success")
return bin_map