From 38b8e87183ef216ae50ef26b7e742a390184445e Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 29 Sep 2022 15:19:15 +0200
Subject: [PATCH 1/7] REFAC: typing (wip)
---
pyotb/core.py | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index d309d85..d68cd1d 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -1,5 +1,6 @@
# -*- coding: utf-8 -*-
"""This module is the core of pyotb."""
+from __future__ import annotations
from pathlib import Path
import numpy as np
@@ -15,7 +16,7 @@ class otbObject:
output_param = ""
@property
- def name(self):
+ def name(self) -> str:
"""Application name that will be printed in logs.
Returns:
@@ -25,7 +26,7 @@ class otbObject:
return self._name or self.app.GetName()
@name.setter
- def name(self, val):
+ def name(self, val: str):
"""Set custom name.
Args:
@@ -35,7 +36,7 @@ class otbObject:
self._name = val
@property
- def dtype(self):
+ def dtype(self) -> int:
"""Expose the pixel type of an output image using numpy convention.
Returns:
@@ -49,7 +50,7 @@ class otbObject:
return None
@property
- def shape(self):
+ def shape(self) -> tuple[int, int, int]:
"""Enables to retrieve the shape of a pyotb object using numpy convention.
Returns:
@@ -60,7 +61,7 @@ class otbObject:
bands = self.app.GetImageNbBands(self.output_param)
return (height, width, bands)
- def write(self, *args, filename_extension="", pixel_type=None, **kwargs):
+ def write(self, *args: dict | str, filename_extension: str="", pixel_type: dict | str=None, **kwargs):
"""Trigger execution, set output pixel type and write the output.
Args:
@@ -136,7 +137,7 @@ class otbObject:
logger.debug('%s: failed to simply write output, executing once again then writing', self.name)
self.app.ExecuteAndWriteOutput()
- def to_numpy(self, preserve_dtype=True, copy=False):
+ def to_numpy(self, preserve_dtype: bool=True, copy: bool=False):
"""Export a pyotb object to numpy array.
Args:
@@ -156,7 +157,7 @@ class otbObject:
return array.copy()
return array
- def to_rasterio(self):
+ def to_rasterio(self) -> tuple(np.ndarray, dict):
"""Export image as a numpy array and its metadata compatible with rasterio.
Returns:
--
GitLab
From f7a262b13e09f912a4acdfdaece09d242097a564 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 11 Jan 2023 22:56:20 +0100
Subject: [PATCH 2/7] DOC: typing hint
---
pyotb/core.py | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index bc6860f..7ea38dc 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -297,7 +297,7 @@ class OTBObject:
for key in keys:
self.app.SetParameterOutputImagePixelType(key, dtype)
- def read_values_at_coords(self, row: int, col: int, bands: int = None):
+ def read_values_at_coords(self, row: int, col: int, bands: int = None) -> list[int | float] | int | float:
"""Get pixel value(s) at a given YX coordinates.
Args:
@@ -329,7 +329,7 @@ class OTBObject:
return data[0]
return data
- def channels_list_from_slice(self, bands: int):
+ def channels_list_from_slice(self, bands: int) -> list[int]:
"""Get list of channels to read values at, from a slice."""
nb_channels = self.shape[2]
start, stop, step = bands.start, bands.stop, bands.step
@@ -806,7 +806,7 @@ class OTBObject:
"""
return self.to_numpy()
- def __array_ufunc__(self, ufunc, method, *inputs, **kwargs):
+ def __array_ufunc__(self, ufunc, method, *inputs, **kwargs) -> OTBObject:
"""This is called whenever a numpy function is called on a pyotb object.
Operation is performed in numpy, then imported back to pyotb with the same georeference as input.
@@ -1049,7 +1049,7 @@ class Operation(OTBObject):
fake_exp = f"({fake_exps[0]} ? {fake_exps[1]} : {fake_exps[2]})"
self.fake_exp_bands.append(fake_exp)
- def get_real_exp(self, fake_exp_bands: str):
+ def get_real_exp(self, fake_exp_bands: str) -> tuple(list[str], str):
"""Generates the BandMathX expression.
Args:
@@ -1073,7 +1073,8 @@ class Operation(OTBObject):
return exp_bands, exp
@staticmethod
- def create_one_input_fake_exp(x: OTBObject | Output | str, band: int, keep_logical: bool = False):
+ def create_one_input_fake_exp(x: OTBObject | Output | str,
+ band: int, keep_logical: bool = False) -> tuple(str, list[OTBObject], int):
"""This an internal function, only to be used by `create_fake_exp`.
Enable to create a fake expression just for one input and one band.
@@ -1130,7 +1131,7 @@ class Operation(OTBObject):
fake_exp = f"{x}b{band}"
return fake_exp, inputs, nb_channels
- def __str__(self):
+ def __str__(self) -> str:
"""Return a nice string representation with operator and object id."""
return f"<pyotb.Operation `{self.operator}` object, id {id(self)}>"
@@ -1215,7 +1216,7 @@ class Input(OTBObject):
self.propagate_dtype()
self.execute()
- def __str__(self):
+ def __str__(self) -> str:
"""Return a nice string representation with file path."""
return f"<pyotb.Input object from {self.path}>"
@@ -1253,7 +1254,7 @@ class Output:
if not self.filepath.parent.exists():
self.filepath.parent.mkdir(parents=True)
- def __str__(self):
+ def __str__(self) -> str:
"""Return a nice string representation with source app name and object id."""
return f"<pyotb.Output {self.source_app.name} object, id {id(self)}>"
--
GitLab
From 7a36939d7910d3eb096bd63bdb4db0ca765e0f17 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 11 Jan 2023 22:58:19 +0100
Subject: [PATCH 3/7] DOC: typing hint
---
pyotb/apps.py | 15 ++++++++-------
pyotb/functions.py | 19 ++++++++++++-------
2 files changed, 20 insertions(+), 14 deletions(-)
diff --git a/pyotb/apps.py b/pyotb/apps.py
index 5e30d0e..a2af7ed 100644
--- a/pyotb/apps.py
+++ b/pyotb/apps.py
@@ -1,5 +1,6 @@
# -*- coding: utf-8 -*-
"""Search for OTB (set env if necessary), subclass core.App for each available application."""
+from __future__ import annotations
import os
import sys
from pathlib import Path
@@ -9,7 +10,7 @@ from .core import OTBObject
from .helpers import logger
-def get_available_applications(as_subprocess=False):
+def get_available_applications(as_subprocess: bool = False) -> list[str]:
"""Find available OTB applications.
Args:
@@ -68,11 +69,11 @@ class App(OTBObject):
self.description = self.app.GetDocLongDescription()
@property
- def used_outputs(self):
+ def used_outputs(self) -> list[str]:
"""List of used application outputs."""
return [getattr(self, key) for key in self.out_param_types if key in self.parameters]
- def find_outputs(self):
+ def find_outputs(self) -> tuple[str]:
"""Find output files on disk using path found in parameters.
Returns:
@@ -91,7 +92,7 @@ class App(OTBObject):
class OTBTFApp(App):
"""Helper for OTBTF."""
@staticmethod
- def set_nb_sources(*args, n_sources=None):
+ def set_nb_sources(*args, n_sources: int = None):
"""Set the number of sources of TensorflowModelServe. Can be either user-defined or deduced from the args.
Args:
@@ -109,11 +110,11 @@ class OTBTFApp(App):
if n_sources >= 1:
os.environ['OTB_TF_NSOURCES'] = str(n_sources)
- def __init__(self, app_name, *args, n_sources=None, **kwargs):
+ def __init__(self, name: str, *args, n_sources: int = None, **kwargs):
"""Constructor for an OTBTFApp object.
Args:
- app_name: name of the OTBTF app
+ name: name of the OTBTF app
*args: arguments (dict). NB: we don't need kwargs because it cannot contain source#.il
n_sources: number of sources. Default is None (resolves the number of sources based on the
content of the dict passed in args, where some 'source' str is found)
@@ -121,7 +122,7 @@ class OTBTFApp(App):
"""
self.set_nb_sources(*args, n_sources=n_sources)
- super().__init__(app_name, *args, **kwargs)
+ super().__init__(name, *args, **kwargs)
AVAILABLE_APPLICATIONS = get_available_applications(as_subprocess=True)
diff --git a/pyotb/functions.py b/pyotb/functions.py
index 669039a..906547f 100644
--- a/pyotb/functions.py
+++ b/pyotb/functions.py
@@ -1,5 +1,6 @@
# -*- coding: utf-8 -*-
"""This module provides a set of functions for pyotb."""
+from __future__ import annotations
import inspect
import os
import sys
@@ -7,18 +8,19 @@ import textwrap
import uuid
from collections import Counter
-from .core import (OTBObject, Input, Operation, LogicalOperation, get_nbchannels)
+from .core import OTBObject, Input, Operation, LogicalOperation, get_nbchannels, Output
from .helpers import logger
-def where(cond, x, y):
+def where(cond: OTBObject | Output | str, x: OTBObject | Output | str | int | float,
+ y: OTBObject | Output | str | int | float) -> Operation:
"""Functionally similar to numpy.where. Where cond is True (!=0), returns x. Else returns y.
Args:
cond: condition, must be a raster (filepath, App, Operation...). If cond is monoband whereas x or y are
multiband, cond channels are expanded to match x & y ones.
- x: value if cond is True. Can be float, int, App, filepath, Operation...
- y: value if cond is False. Can be float, int, App, filepath, Operation...
+ x: value if cond is True. Can be: float, int, App, filepath, Operation...
+ y: value if cond is False. Can be: float, int, App, filepath, Operation...
Returns:
an output where pixels are x if cond is True, else y
@@ -61,7 +63,8 @@ def where(cond, x, y):
return operation
-def clip(a, a_min, a_max):
+def clip(a: OTBObject | Output | str, a_min: OTBObject | Output | str | int | float,
+ a_max: OTBObject | Output | str | int | float):
"""Clip values of image in a range of values.
Args:
@@ -321,8 +324,10 @@ def run_tf_function(func):
return wrapper
-def define_processing_area(*args, window_rule='intersection', pixel_size_rule='minimal', interpolator='nn',
- reference_window_input=None, reference_pixel_size_input=None):
+def define_processing_area(*args, window_rule: str = 'intersection', pixel_size_rule: str = 'minimal',
+ interpolator: str = 'nn',
+ reference_window_input: dict = None, reference_pixel_size_input: str = None) -> list[
+ OTBObject]:
"""Given several inputs, this function handles the potential resampling and cropping to same extent.
WARNING: Not fully implemented / tested
--
GitLab
From d9ca23ae55b32b828d52c0beb8ebd617687ecd8e Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 11 Jan 2023 23:00:37 +0100
Subject: [PATCH 4/7] DOC: typing hint
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 7ea38dc..1208ac9 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -673,7 +673,7 @@ class OTBObject:
return NotImplemented # this enables to fallback on numpy emulation thanks to __array_ufunc__
return Operation("/", other, self)
- def __abs__(self, other: OTBObject | Output | str | int | float) -> Operation:
+ def __abs__(self) -> Operation:
"""Overrides the default abs operator and flavours it with BandMathX.
Returns:
--
GitLab
From efd8f6ebd682987b2db4573ce762f96276076236 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 11 Jan 2023 23:03:24 +0100
Subject: [PATCH 5/7] DOC: typing hint
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 1208ac9..88496b6 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -449,7 +449,7 @@ class OTBObject:
for arg in args:
if isinstance(arg, dict):
kwargs.update(arg)
- elif isinstance(arg, (str, OTBObject, list)) and is_key_list(self, self.key_input):
+ elif isinstance(arg, (str, OTBObject)) or isinstance(arg, list) and is_key_list(self, self.key_input):
kwargs.update({self.key_input: arg})
return kwargs
--
GitLab
From de049834402058a055d9ab1ba675f86516ea518c Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 11 Jan 2023 23:08:06 +0100
Subject: [PATCH 6/7] DOC: typing hint
---
pyotb/functions.py | 5 ++---
1 file changed, 2 insertions(+), 3 deletions(-)
diff --git a/pyotb/functions.py b/pyotb/functions.py
index 906547f..aa161e6 100644
--- a/pyotb/functions.py
+++ b/pyotb/functions.py
@@ -325,9 +325,8 @@ def run_tf_function(func):
def define_processing_area(*args, window_rule: str = 'intersection', pixel_size_rule: str = 'minimal',
- interpolator: str = 'nn',
- reference_window_input: dict = None, reference_pixel_size_input: str = None) -> list[
- OTBObject]:
+ interpolator: str = 'nn', reference_window_input: dict = None,
+ reference_pixel_size_input: str = None) -> list[OTBObject]:
"""Given several inputs, this function handles the potential resampling and cropping to same extent.
WARNING: Not fully implemented / tested
--
GitLab
From d75905f86847a514acb2884374734d38f63bb6f5 Mon Sep 17 00:00:00 2001
From: Vincent Delbar <vincent.delbar@latelescop.fr>
Date: Fri, 13 Jan 2023 11:35:06 +0100
Subject: [PATCH 7/7] ENH: type hints for helpers.py
---
pyotb/helpers.py | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/pyotb/helpers.py b/pyotb/helpers.py
index 742fee1..d38dfb3 100644
--- a/pyotb/helpers.py
+++ b/pyotb/helpers.py
@@ -26,7 +26,7 @@ logger_handler.setLevel(getattr(logging, LOG_LEVEL))
logger.addHandler(logger_handler)
-def set_logger_level(level):
+def set_logger_level(level: str):
"""Allow user to change the current logging level.
Args:
@@ -36,7 +36,7 @@ def set_logger_level(level):
logger_handler.setLevel(getattr(logging, level))
-def find_otb(prefix=OTB_ROOT, scan=True, scan_userdir=True):
+def find_otb(prefix: str = OTB_ROOT, scan: bool = True, scan_userdir: bool = True):
"""Try to load OTB bindings or scan system, help user in case of failure, set env variables.
Path precedence : OTB_ROOT > python bindings directory
@@ -98,7 +98,7 @@ def find_otb(prefix=OTB_ROOT, scan=True, scan_userdir=True):
raise SystemExit("Failed to import OTB. Exiting.") from e
-def set_environment(prefix):
+def set_environment(prefix: str):
"""Set environment variables (before OTB import), raise error if anything is wrong.
Args:
@@ -156,7 +156,7 @@ def set_environment(prefix):
os.environ["PROJ_LIB"] = proj_lib
-def __find_lib(prefix=None, otb_module=None):
+def __find_lib(prefix: str = None, otb_module=None):
"""Try to find OTB external libraries directory.
Args:
@@ -187,7 +187,7 @@ def __find_lib(prefix=None, otb_module=None):
return None
-def __find_python_api(lib_dir):
+def __find_python_api(lib_dir: Path):
"""Try to find the python path.
Args:
@@ -206,7 +206,7 @@ def __find_python_api(lib_dir):
return None
-def __find_apps_path(lib_dir):
+def __find_apps_path(lib_dir: Path):
"""Try to find the OTB applications path.
Args:
@@ -225,7 +225,7 @@ def __find_apps_path(lib_dir):
return ""
-def __find_otb_root(scan_userdir=False):
+def __find_otb_root(scan_userdir: bool = False):
"""Search for OTB root directory in well known locations.
Args:
@@ -271,7 +271,7 @@ def __find_otb_root(scan_userdir=False):
return prefix
-def __suggest_fix_import(error_message, prefix):
+def __suggest_fix_import(error_message: str, prefix: str):
"""Help user to fix the OTB installation with appropriate log messages."""
logger.critical("An error occurred while importing OTB Python API")
logger.critical("OTB error message was '%s'", error_message)
--
GitLab