From 8827e4a250603efc5f9b63ed9c1fa937de866b16 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:36:01 +0200
Subject: [PATCH 01/23] WIP: implement extended filenames as dict
---
pyotb/core.py | 312 ++++++++++++++++++++++++++++++--------------------
1 file changed, 188 insertions(+), 124 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 06da0c7..268b284 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -87,7 +87,7 @@ class OTBObject(ABC):
return App("ComputeImagesStatistics", self, quiet=True).data
def get_values_at_coords(
- self, row: int, col: int, bands: int = None
+ self, row: int, col: int, bands: int = None
) -> list[int | float] | int | float:
"""Get pixel value(s) at a given YX coordinates.
@@ -101,7 +101,8 @@ class OTBObject(ABC):
"""
channels = []
- app = App("PixelValue", self, coordx=col, coordy=row, frozen=True, quiet=True)
+ app = App("PixelValue", self, coordx=col, coordy=row, frozen=True,
+ quiet=True)
if bands is not None:
if isinstance(bands, int):
if bands < 0:
@@ -115,7 +116,8 @@ class OTBObject(ABC):
)
if channels:
app.app.Execute()
- app.set_parameters({"cl": [f"Channel{n + 1}" for n in channels]})
+ app.set_parameters(
+ {"cl": [f"Channel{n + 1}" for n in channels]})
app.execute()
data = literal_eval(app.app.GetParameterString("value"))
return data[0] if len(channels) == 1 else data
@@ -124,8 +126,10 @@ class OTBObject(ABC):
"""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
- start = nb_channels + start if isinstance(start, int) and start < 0 else start
- stop = nb_channels + stop if isinstance(stop, int) and stop < 0 else stop
+ start = nb_channels + start if isinstance(start,
+ int) and start < 0 else start
+ stop = nb_channels + stop if isinstance(stop,
+ int) and stop < 0 else stop
step = 1 if step is None else step
if start is not None and stop is not None:
return list(range(start, stop, step))
@@ -140,7 +144,7 @@ class OTBObject(ABC):
)
def export(
- self, key: str = None, preserve_dtype: bool = True
+ self, key: str = None, preserve_dtype: bool = True
) -> dict[str, dict[str, np.ndarray]]:
"""Export a specific output image as numpy array and store it in object exports_dic.
@@ -158,13 +162,15 @@ class OTBObject(ABC):
if key not in self.exports_dic:
self.exports_dic[key] = self.app.ExportImage(key)
if preserve_dtype:
- self.exports_dic[key]["array"] = self.exports_dic[key]["array"].astype(
+ self.exports_dic[key]["array"] = self.exports_dic[key][
+ "array"].astype(
self.dtype
)
return self.exports_dic[key]
def to_numpy(
- self, key: str = None, preserve_dtype: bool = True, copy: bool = False
+ self, key: str = None, preserve_dtype: bool = True,
+ copy: bool = False
) -> np.ndarray:
"""Export a pyotb object to numpy array.
@@ -193,7 +199,8 @@ class OTBObject(ABC):
profile = {}
array = self.to_numpy(preserve_dtype=True, copy=False)
proj = self.app.GetImageProjection(self.output_image_key)
- profile.update({"crs": proj, "dtype": array.dtype, "transform": self.transform})
+ profile.update(
+ {"crs": proj, "dtype": array.dtype, "transform": self.transform})
height, width, count = array.shape
profile.update({"count": count, "height": height, "width": width})
return np.moveaxis(array, 2, 0), profile
@@ -294,7 +301,8 @@ class OTBObject(ABC):
"""Logical or."""
return self.__create_operator(LogicalOperation, "||", self, other)
- def __and__(self, other: OTBObject | str | int | float) -> LogicalOperation:
+ def __and__(self,
+ other: OTBObject | str | int | float) -> LogicalOperation:
"""Logical and."""
return self.__create_operator(LogicalOperation, "&&", self, other)
@@ -390,7 +398,7 @@ class OTBObject(ABC):
return self.get_values_at_coords(row, col, channels)
# Slicing
if not isinstance(key, tuple) or (
- isinstance(key, tuple) and (len(key) < 2 or len(key) > 3)
+ isinstance(key, tuple) and (len(key) < 2 or len(key) > 3)
):
raise ValueError(
f'"{key}" cannot be interpreted as valid slicing. Slicing should be 2D or 3D.'
@@ -446,13 +454,13 @@ class App(OTBObject):
]
def __init__(
- self,
- appname: str,
- *args,
- frozen: bool = False,
- quiet: bool = False,
- name: str = "",
- **kwargs,
+ self,
+ appname: str,
+ *args,
+ frozen: bool = False,
+ quiet: bool = False,
+ name: str = "",
+ **kwargs,
):
"""Common constructor for OTB applications. Handles in-memory connection between apps.
@@ -502,8 +510,9 @@ class App(OTBObject):
self.set_parameters(*args, **kwargs)
# Create Output image objects
for key in filter(
- lambda k: self._out_param_types[k] == otb.ParameterType_OutputImage,
- self._out_param_types,
+ lambda k: self._out_param_types[
+ k] == otb.ParameterType_OutputImage,
+ self._out_param_types,
):
self.outputs[key] = Output(self, key, self._settings.get(key))
if not self.frozen:
@@ -524,7 +533,8 @@ class App(OTBObject):
@property
def parameters(self):
"""Return used OTB application parameters."""
- return {**self._auto_parameters, **self.app.GetParameters(), **self._settings}
+ return {**self._auto_parameters, **self.app.GetParameters(),
+ **self._settings}
@property
def exports_dic(self) -> dict[str, dict]:
@@ -534,7 +544,8 @@ class App(OTBObject):
def __is_one_of_types(self, key: str, param_types: list[int]) -> bool:
"""Helper to factor is_input and is_output."""
if key not in self._all_param_types:
- raise KeyError(f"key {key} not found in the application parameters types")
+ raise KeyError(
+ f"key {key} not found in the application parameters types")
return self._all_param_types[key] in param_types
def is_input(self, key: str) -> bool:
@@ -547,7 +558,8 @@ class App(OTBObject):
True if the parameter is an input, else False
"""
- return self.__is_one_of_types(key=key, param_types=self.INPUT_PARAM_TYPES)
+ return self.__is_one_of_types(key=key,
+ param_types=self.INPUT_PARAM_TYPES)
def is_output(self, key: str) -> bool:
"""Returns True if the key is an output.
@@ -559,7 +571,8 @@ class App(OTBObject):
True if the parameter is an output, else False
"""
- return self.__is_one_of_types(key=key, param_types=self.OUTPUT_PARAM_TYPES)
+ return self.__is_one_of_types(key=key,
+ param_types=self.OUTPUT_PARAM_TYPES)
def is_key_list(self, key: str) -> bool:
"""Check if a parameter key is an input parameter list."""
@@ -683,7 +696,8 @@ class App(OTBObject):
dtype = get_pixel_type(param)
except (TypeError, RuntimeError):
logger.warning(
- '%s: unable to identify pixel type of key "%s"', self.name, param
+ '%s: unable to identify pixel type of key "%s"', self.name,
+ param
)
return
if target_key:
@@ -699,7 +713,8 @@ class App(OTBObject):
def execute(self):
"""Execute and write to disk if any output parameter has been set during init."""
- logger.debug("%s: run execute() with parameters=%s", self.name, self.parameters)
+ logger.debug("%s: run execute() with parameters=%s", self.name,
+ self.parameters)
self._time_start = perf_counter()
try:
self.app.Execute()
@@ -727,28 +742,36 @@ class App(OTBObject):
self._time_end = perf_counter()
def write(
- self,
- path: str | Path | dict[str, str] = None,
- pixel_type: dict[str, str] | str = None,
- preserve_dtype: bool = False,
- ext_fname: str = "",
- **kwargs,
+ self,
+ path: str | Path | dict[str, str] = None,
+ pixel_type: dict[str, str] | str = None,
+ preserve_dtype: bool = False,
+ ext_fname: str | dict[str, str] | dict[str, int] | dict[
+ str, float] = None,
+ **kwargs,
) -> bool:
"""Set output pixel type and write the output raster files.
Args:
- path: Can be : - filepath, useful when there is only one output, e.g. 'output.tif'
- - dictionary containing key-arguments enumeration. Useful when a key contains
- non-standard characters such as a point, e.g. {'io.out':'output.tif'}
- - None if output file was passed during App init
- ext_fname: Optional, an extended filename as understood by OTB (e.g. "&gdal:co:TILED=YES")
- Will be used for all outputs (Default value = "")
- pixel_type: Can be : - dictionary {out_param_key: pixeltype} when specifying for several outputs
- - str (e.g. 'uint16') or otbApplication.ImagePixelType_... When there are several
- outputs, all outputs are written with this unique type.
- Valid pixel types are uint8, uint16, uint32, int16, int32, float, double,
- cint16, cint32, cfloat, cdouble. (Default value = None)
- preserve_dtype: propagate main input pixel type to outputs, in case pixel_type is None
+ path: Can be :
+ - filepath, useful when there is only one output, e.g.
+ 'output.tif'
+ - dictionary containing key-arguments enumeration. Useful when
+ a key contains non-standard characters such as a point, e.g.
+ {'io.out':'output.tif'}
+ - None if output file was passed during App init
+ ext_fname: Optional, an extended filename as understood by OTB
+ (e.g. "&gdal:co:TILED=YES") or a dict of key/value. Will be
+ used for all outputs.
+ pixel_type: Can be :
+ - dictionary {out_param_key: pixeltype} when specifying for
+ several outputs
+ - str (e.g. 'uint16') or otbApplication.ImagePixelType_...
+ When there are several outputs, all outputs are written with
+ this unique type. Valid pixel types are uint8, uint16, uint32,
+ int16, int32, float, double, cint16, cint32, cfloat, cdouble.
+ preserve_dtype: propagate main input pixel type to outputs, in
+ case pixel_type is None
**kwargs: keyword arguments e.g. out='output.tif'
Returns:
@@ -767,28 +790,47 @@ class App(OTBObject):
elif isinstance(path, (str, Path)) and self.output_key:
kwargs.update({self.output_key: str(path)})
elif path is not None:
- raise TypeError(f"{self.name}: unsupported filepath type ({type(path)})")
- if not (kwargs or any(k in self._settings for k in self._out_param_types)):
+ raise TypeError(
+ f"{self.name}: unsupported filepath type ({type(path)})")
+ if not (kwargs or any(
+ k in self._settings for k in self._out_param_types)):
raise KeyError(
f"{self.name}: at least one filepath is required, if not provided during App init"
)
parameters = kwargs.copy()
# Append filename extension to filenames
+ assert isinstance(ext_fname, (dict, str))
if ext_fname:
- logger.debug(
- "%s: using extended filename for outputs: %s", self.name, ext_fname
- )
- if not ext_fname.startswith("?"):
- ext_fname = "?&" + ext_fname
- elif not ext_fname.startswith("?&"):
- ext_fname = "?&" + ext_fname[1:]
- for key, value in kwargs.items():
- if (
- self._out_param_types[key] == otb.ParameterType_OutputImage
- and "?" not in value
- ):
- parameters[key] = value + ext_fname
+
+ def _str2dict(ext_str):
+ """Function that converts str to dict."""
+ return dict(
+ kv for pair in ext_str.split("&")
+ if len(kv := pair.split("=")) == 2
+ )
+
+ if isinstance(ext_fname, str):
+ # transform str to dict
+ ext_fname = _str2dict(ext_fname)
+
+ logger.debug("%s: extended filename for outputs: %s", self.name)
+ for key, ext in ext_fname.items():
+ logger.debug("%s: %s", key, ext)
+
+ for key, filepath in kwargs.items():
+ if self._out_param_types[key] == otb.ParameterType_OutputImage:
+ # grab already set extended filename key/values
+ already_set_ext = _str2dict(filepath.split("?&")[0]) \
+ if "?&" in filepath else {}
+
+ # transform dict to str
+ ext_fname_str = "&".join([
+ f"{k}={v}" for k, v in ext_fname.items()
+ if k not in already_set_ext
+ ])
+ parameters[key] = f"{filepath}?{ext_fname_str}"
+
# Manage output pixel types
data_types = {}
if pixel_type:
@@ -796,14 +838,17 @@ class App(OTBObject):
dtype = parse_pixel_type(pixel_type)
type_name = self.app.ConvertPixelTypeToNumpy(dtype)
logger.debug(
- '%s: output(s) will be written with type "%s"', self.name, type_name
+ '%s: output(s) will be written with type "%s"', self.name,
+ type_name
)
for key in parameters:
- if self._out_param_types[key] == otb.ParameterType_OutputImage:
+ if self._out_param_types[
+ key] == otb.ParameterType_OutputImage:
data_types[key] = dtype
elif isinstance(pixel_type, dict):
data_types = {
- key: parse_pixel_type(dtype) for key, dtype in pixel_type.items()
+ key: parse_pixel_type(dtype) for key, dtype in
+ pixel_type.items()
}
elif preserve_dtype:
self.propagate_dtype() # all outputs will have the same type as the main input raster
@@ -836,7 +881,8 @@ class App(OTBObject):
return bool(files) and not missing
# Private functions
- def __parse_args(self, args: list[str | OTBObject | dict | list]) -> dict[str, Any]:
+ def __parse_args(self, args: list[str | OTBObject | dict | list]) -> dict[
+ str, Any]:
"""Gather all input arguments in kwargs dict.
Args:
@@ -851,15 +897,16 @@ class App(OTBObject):
if isinstance(arg, dict):
kwargs.update(arg)
elif (
- isinstance(arg, (str, OTBObject))
- or isinstance(arg, list)
- and self.is_key_list(self.input_key)
+ isinstance(arg, (str, OTBObject))
+ or isinstance(arg, list)
+ and self.is_key_list(self.input_key)
):
kwargs.update({self.input_key: arg})
return kwargs
def __set_param(
- self, key: str, obj: list | tuple | OTBObject | otb.Application | list[Any]
+ self, key: str,
+ obj: list | tuple | OTBObject | otb.Application | list[Any]
):
"""Set one parameter, decide which otb.Application method to use depending on target object."""
if obj is None or (isinstance(obj, (list, tuple)) and not obj):
@@ -869,11 +916,11 @@ class App(OTBObject):
if isinstance(obj, OTBObject):
self.app.ConnectImage(key, obj.app, obj.output_image_key)
elif isinstance(
- obj, otb.Application
+ obj, otb.Application
): # this is for backward comp with plain OTB
self.app.ConnectImage(key, obj, get_out_images_param_keys(obj)[0])
elif (
- key == "ram"
+ key == "ram"
): # SetParameterValue in OTB<7.4 doesn't work for ram parameter cf gitlab OTB issue 2200
self.app.SetParameterInt("ram", int(obj))
elif not isinstance(obj, list): # any other parameters (str, int...)
@@ -885,9 +932,10 @@ class App(OTBObject):
if isinstance(inp, OTBObject):
self.app.ConnectImage(key, inp.app, inp.output_image_key)
elif isinstance(
- inp, otb.Application
+ inp, otb.Application
): # this is for backward comp with plain OTB
- self.app.ConnectImage(key, obj, get_out_images_param_keys(inp)[0])
+ self.app.ConnectImage(key, obj,
+ get_out_images_param_keys(inp)[0])
else: # here `input` should be an image filepath
# Append `input` to the list, do not overwrite any previously set element of the image list
self.app.AddParameterStringList(key, inp)
@@ -902,8 +950,9 @@ class App(OTBObject):
continue
value = self.app.GetParameterValue(key)
# TODO: here we *should* use self.app.IsParameterEnabled, but it seems broken
- if isinstance(value, otb.ApplicationProxy) and self.app.HasAutomaticValue(
- key
+ if isinstance(value,
+ otb.ApplicationProxy) and self.app.HasAutomaticValue(
+ key
):
try:
value = str(
@@ -914,7 +963,8 @@ class App(OTBObject):
except RuntimeError:
continue # grouped parameters
# Save static output data (ReadImageInfo, ComputeImageStatistics, etc.)
- elif self.app.GetParameterRole(key) == 1 and bool(value) or value == 0:
+ elif self.app.GetParameterRole(key) == 1 and bool(
+ value) or value == 0:
if isinstance(value, str):
try:
value = literal_eval(value)
@@ -923,7 +973,8 @@ class App(OTBObject):
self.data[key] = value
# Special functions
- def __getitem__(self, key: str) -> Any | list[int | float] | int | float | Slicer:
+ def __getitem__(self, key: str) -> Any | list[
+ int | float] | int | float | Slicer:
"""This function is called when we use App()[...].
We allow to return attr if key is a parameter, or call OTBObject __getitem__ for pixel values or Slicer
@@ -937,7 +988,8 @@ class App(OTBObject):
return self.outputs[key]
if key in self.parameters:
return self.parameters[key]
- raise KeyError(f"{self.name}: unknown or undefined parameter '{key}'")
+ raise KeyError(
+ f"{self.name}: unknown or undefined parameter '{key}'")
raise TypeError(
f"{self.name}: cannot access object item or slice using {type(key)} object"
)
@@ -947,11 +999,11 @@ class Slicer(App):
"""Slicer objects i.e. when we call something like raster[:, :, 2] from Python."""
def __init__(
- self,
- obj: OTBObject,
- rows: slice,
- cols: slice,
- channels: slice | list[int] | int,
+ self,
+ obj: OTBObject,
+ rows: slice,
+ cols: slice,
+ channels: slice | list[int] | int,
):
"""Create a slicer object, that can be used directly for writing or inside a BandMath.
@@ -1018,9 +1070,10 @@ class Slicer(App):
) # subtract 1 to respect python convention
spatial_slicing = True
# These are some attributes when the user simply wants to extract *one* band to be used in an Operation
- if not spatial_slicing and isinstance(channels, list) and len(channels) == 1:
+ if not spatial_slicing and isinstance(channels, list) and len(
+ channels) == 1:
self.one_band_sliced = (
- channels[0] + 1
+ channels[0] + 1
) # OTB convention: channels start at 1
self.input = obj
@@ -1051,7 +1104,8 @@ class Operation(App):
"""
- def __init__(self, operator: str, *inputs, nb_bands: int = None, name: str = None):
+ def __init__(self, operator: str, *inputs, nb_bands: int = None,
+ name: str = None):
"""Given some inputs and an operator, this function enables to transform this into an OTB application.
Operations generally involve 2 inputs (+, -...). It can have only 1 input for `abs` operator.
@@ -1098,10 +1152,10 @@ class Operation(App):
)
def build_fake_expressions(
- self,
- operator: str,
- inputs: list[OTBObject | str | int | float],
- nb_bands: int = None,
+ self,
+ operator: str,
+ inputs: list[OTBObject | str | int | float],
+ nb_bands: int = None,
):
"""Create a list of 'fake' expressions, one for each band.
@@ -1122,8 +1176,8 @@ class Operation(App):
# For any other operations, the output number of bands is the same as inputs
else:
if any(
- isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
- for inp in inputs
+ isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
+ for inp in inputs
):
nb_bands = 1
else:
@@ -1134,9 +1188,10 @@ class Operation(App):
]
# check that all inputs have the same nb of bands
if len(nb_bands_list) > 1 and not all(
- x == nb_bands_list[0] for x in nb_bands_list
+ x == nb_bands_list[0] for x in nb_bands_list
):
- raise ValueError("All images do not have the same number of bands")
+ raise ValueError(
+ "All images do not have the same number of bands")
nb_bands = nb_bands_list[0]
# Create a list of fake expressions, each item of the list corresponding to one band
@@ -1171,7 +1226,7 @@ class Operation(App):
# the false expression stores the expression 2 * str(input1) + str(input2)
fake_exp = f"({expressions[0]} {operator} {expressions[1]})"
elif (
- len(inputs) == 3 and operator == "?"
+ len(inputs) == 3 and operator == "?"
): # this is only for ternary expression
fake_exp = f"({expressions[0]} ? {expressions[1]} : {expressions[2]})"
self.fake_exp_bands.append(fake_exp)
@@ -1193,14 +1248,15 @@ class Operation(App):
one_band_exp = one_band_fake_exp
for inp in self.inputs:
# Replace the name of in-memory object (e.g. '<pyotb.App object>b1' by 'im1b1')
- one_band_exp = one_band_exp.replace(repr(inp), self.im_dic[repr(inp)])
+ one_band_exp = one_band_exp.replace(repr(inp),
+ self.im_dic[repr(inp)])
exp_bands.append(one_band_exp)
# Form the final expression (e.g. 'im1b1 + 1; im1b2 + 1')
return exp_bands, ";".join(exp_bands)
@staticmethod
def make_fake_exp(
- x: OTBObject | str, band: int, keep_logical: bool = False
+ x: OTBObject | str, band: int, keep_logical: bool = False
) -> tuple[str, list[OTBObject], int]:
"""This an internal function, only to be used by `build_fake_expressions`.
@@ -1223,7 +1279,8 @@ class Operation(App):
# Special case for one-band slicer
if isinstance(x, Slicer) and hasattr(x, "one_band_sliced"):
if keep_logical and isinstance(x.input, LogicalOperation):
- fake_exp = x.input.logical_fake_exp_bands[x.one_band_sliced - 1]
+ fake_exp = x.input.logical_fake_exp_bands[
+ x.one_band_sliced - 1]
inputs, nb_channels = x.input.inputs, x.input.nb_channels
elif isinstance(x.input, Operation):
# Keep only one band of the expression
@@ -1275,16 +1332,17 @@ class LogicalOperation(Operation):
"""
self.logical_fake_exp_bands = []
- super().__init__(operator, *inputs, nb_bands=nb_bands, name="LogicalOperation")
+ super().__init__(operator, *inputs, nb_bands=nb_bands,
+ name="LogicalOperation")
self.logical_exp_bands, self.logical_exp = self.get_real_exp(
self.logical_fake_exp_bands
)
def build_fake_expressions(
- self,
- operator: str,
- inputs: list[OTBObject | str | int | float],
- nb_bands: int = None,
+ self,
+ operator: str,
+ inputs: list[OTBObject | str | int | float],
+ nb_bands: int = None,
):
"""Create a list of 'fake' expressions, one for each band.
@@ -1299,8 +1357,8 @@ class LogicalOperation(Operation):
"""
# For any other operations, the output number of bands is the same as inputs
if any(
- isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
- for inp in inputs
+ isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
+ for inp in inputs
):
nb_bands = 1
else:
@@ -1311,9 +1369,10 @@ class LogicalOperation(Operation):
]
# check that all inputs have the same nb of bands
if len(nb_bands_list) > 1 and not all(
- x == nb_bands_list[0] for x in nb_bands_list
+ x == nb_bands_list[0] for x in nb_bands_list
):
- raise ValueError("All images do not have the same number of bands")
+ raise ValueError(
+ "All images do not have the same number of bands")
nb_bands = nb_bands_list[0]
# Create a list of fake exp, each item of the list corresponding to one band
for i, band in enumerate(range(1, nb_bands + 1)):
@@ -1366,11 +1425,11 @@ class Output(OTBObject):
_filepath: str | Path = None
def __init__(
- self,
- pyotb_app: App,
- param_key: str = None,
- filepath: str = None,
- mkdir: bool = True,
+ self,
+ pyotb_app: App,
+ param_key: str = None,
+ filepath: str = None,
+ mkdir: bool = True,
):
"""Constructor for an Output object.
@@ -1417,7 +1476,8 @@ class Output(OTBObject):
@filepath.setter
def filepath(self, path: str):
if isinstance(path, str):
- if path and not path.startswith(("/vsi", "http://", "https://", "ftp://")):
+ if path and not path.startswith(
+ ("/vsi", "http://", "https://", "ftp://")):
path = Path(path.split("?")[0])
self._filepath = path
@@ -1439,7 +1499,8 @@ class Output(OTBObject):
return self.parent_pyotb_app.write(
{self.output_image_key: self.filepath}, **kwargs
)
- return self.parent_pyotb_app.write({self.output_image_key: filepath}, **kwargs)
+ return self.parent_pyotb_app.write({self.output_image_key: filepath},
+ **kwargs)
def __str__(self) -> str:
"""Return string representation of Output filepath."""
@@ -1496,12 +1557,13 @@ def get_nbchannels(inp: str | Path | OTBObject) -> int:
info = App("ReadImageInfo", inp, quiet=True)
return info["numberbands"]
except (
- RuntimeError
+ RuntimeError
) as info_err: # this happens when we pass a str that is not a filepath
raise TypeError(
f"Could not get the number of channels file '{inp}' ({info_err})"
) from info_err
- raise TypeError(f"Can't read number of channels of type '{type(inp)}' object {inp}")
+ raise TypeError(
+ f"Can't read number of channels of type '{type(inp)}' object {inp}")
def get_pixel_type(inp: str | Path | OTBObject) -> str:
@@ -1522,14 +1584,15 @@ def get_pixel_type(inp: str | Path | OTBObject) -> str:
info = App("ReadImageInfo", inp, quiet=True)
datatype = info["datatype"] # which is such as short, float...
except (
- RuntimeError
+ RuntimeError
) as info_err: # this happens when we pass a str that is not a filepath
raise TypeError(
f"Could not get the pixel type of `{inp}` ({info_err})"
) from info_err
if datatype:
return parse_pixel_type(datatype)
- raise TypeError(f"Could not get the pixel type of {type(inp)} object {inp}")
+ raise TypeError(
+ f"Could not get the pixel type of {type(inp)} object {inp}")
def parse_pixel_type(pixel_type: str | int) -> int:
@@ -1559,7 +1622,8 @@ def parse_pixel_type(pixel_type: str | int) -> int:
if pixel_type in datatype_to_pixeltype.values():
return getattr(otb, f"ImagePixelType_{pixel_type}")
if pixel_type in datatype_to_pixeltype:
- return getattr(otb, f"ImagePixelType_{datatype_to_pixeltype[pixel_type]}")
+ return getattr(otb,
+ f"ImagePixelType_{datatype_to_pixeltype[pixel_type]}")
raise KeyError(
f"Unknown data type `{pixel_type}`. Available ones: {datatype_to_pixeltype}"
)
@@ -1578,9 +1642,9 @@ def get_out_images_param_keys(app: OTBObject) -> list[str]:
def summarize(
- obj: App | Output | Any,
- strip_input_paths: bool = False,
- strip_output_paths: bool = False,
+ obj: App | Output | Any,
+ strip_input_paths: bool = False,
+ strip_output_paths: bool = False,
) -> dict[str, str | dict[str, Any]]:
"""Recursively summarize parameters of an App or Output object and its parents.
@@ -1614,10 +1678,10 @@ def summarize(
parameters = {}
for key, param in obj.parameters.items():
if (
- strip_input_paths
- and obj.is_input(key)
- or strip_output_paths
- and obj.is_output(key)
+ strip_input_paths
+ and obj.is_input(key)
+ or strip_output_paths
+ and obj.is_output(key)
):
parameters[key] = (
[strip_path(p) for p in param]
--
GitLab
From 437eb5d003a946b1980de2f45756c294599fa3e0 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:46:26 +0200
Subject: [PATCH 02/23] WIP: implement extended filenames as dict
---
pyotb/core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 268b284..c50ca4d 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -800,9 +800,9 @@ class App(OTBObject):
parameters = kwargs.copy()
# Append filename extension to filenames
- assert isinstance(ext_fname, (dict, str))
if ext_fname:
-
+ assert isinstance(ext_fname, (dict, str))
+
def _str2dict(ext_str):
"""Function that converts str to dict."""
return dict(
--
GitLab
From 9beba5f4f0b5d1b72da13baf7b758aa1a406b357 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:52:51 +0200
Subject: [PATCH 03/23] WIP: implement extended filenames as dict
---
pyotb/core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index c50ca4d..af667aa 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -802,7 +802,7 @@ class App(OTBObject):
# Append filename extension to filenames
if ext_fname:
assert isinstance(ext_fname, (dict, str))
-
+
def _str2dict(ext_str):
"""Function that converts str to dict."""
return dict(
@@ -829,7 +829,7 @@ class App(OTBObject):
f"{k}={v}" for k, v in ext_fname.items()
if k not in already_set_ext
])
- parameters[key] = f"{filepath}?{ext_fname_str}"
+ parameters[key] = f"{filepath}?&{ext_fname_str}"
# Manage output pixel types
data_types = {}
--
GitLab
From 4ac0b869bc22a54489736a0ea5521aeeb0720fe7 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:56:15 +0200
Subject: [PATCH 04/23] ADD: test for extended filename
---
tests/test_core.py | 19 ++++++++++++++++++-
1 file changed, 18 insertions(+), 1 deletion(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 99b21de..b19e92b 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -1,6 +1,5 @@
import pytest
-import pyotb
from tests_data import *
@@ -111,6 +110,24 @@ def test_write():
INPUT["out"].filepath.unlink()
+def test_ext_fname():
+ assert INPUT.write("/tmp/test_write.tif", ext_fname="nodata=0")
+ assert INPUT.write("/tmp/test_write.tif", ext_fname={"nodata": "0"})
+ assert INPUT.write("/tmp/test_write.tif", ext_fname={"nodata": 0})
+ assert INPUT.write(
+ "/tmp/test_write.tif",
+ ext_fname={
+ "nodata": 0,
+ "gdal:co:COMPRESS": "DEFLATE"
+ }
+ )
+ assert INPUT.write(
+ "/tmp/test_write.tif",
+ ext_fname="nodata=0&gdal:co:COMPRESS=DEFLATE"
+ )
+ INPUT["out"].filepath.unlink()
+
+
def test_frozen_app_write():
app = pyotb.BandMath(INPUT, exp="im1b1", frozen=True)
assert app.write("/tmp/test_frozen_app_write.tif")
--
GitLab
From c37e717fa6b4ad0400b06ad7499e4893c5f3b3e7 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:56:31 +0200
Subject: [PATCH 05/23] DOC: pydocstyle
---
pyotb/core.py | 7 +++----
1 file changed, 3 insertions(+), 4 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index af667aa..0cc74a5 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -802,19 +802,18 @@ class App(OTBObject):
# Append filename extension to filenames
if ext_fname:
assert isinstance(ext_fname, (dict, str))
-
def _str2dict(ext_str):
"""Function that converts str to dict."""
return dict(
- kv for pair in ext_str.split("&")
- if len(kv := pair.split("=")) == 2
+ keyval for pair in ext_str.split("&")
+ if len(keyval := pair.split("=")) == 2
)
if isinstance(ext_fname, str):
# transform str to dict
ext_fname = _str2dict(ext_fname)
- logger.debug("%s: extended filename for outputs: %s", self.name)
+ logger.debug("%s: extended filename for outputs:", self.name)
for key, ext in ext_fname.items():
logger.debug("%s: %s", key, ext)
--
GitLab
From 3c4459a5c0d4a8150e5209b2dddba9bc17c4cc24 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 10:07:41 +0200
Subject: [PATCH 06/23] STY: back to original indentation
---
pyotb/core.py | 269 +++++++++++++++++++++-----------------------------
1 file changed, 111 insertions(+), 158 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 0cc74a5..b776a3d 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -87,7 +87,7 @@ class OTBObject(ABC):
return App("ComputeImagesStatistics", self, quiet=True).data
def get_values_at_coords(
- self, row: int, col: int, bands: int = None
+ self, row: int, col: int, bands: int = None
) -> list[int | float] | int | float:
"""Get pixel value(s) at a given YX coordinates.
@@ -101,8 +101,7 @@ class OTBObject(ABC):
"""
channels = []
- app = App("PixelValue", self, coordx=col, coordy=row, frozen=True,
- quiet=True)
+ app = App("PixelValue", self, coordx=col, coordy=row, frozen=True, quiet=True)
if bands is not None:
if isinstance(bands, int):
if bands < 0:
@@ -116,8 +115,7 @@ class OTBObject(ABC):
)
if channels:
app.app.Execute()
- app.set_parameters(
- {"cl": [f"Channel{n + 1}" for n in channels]})
+ app.set_parameters({"cl": [f"Channel{n + 1}" for n in channels]})
app.execute()
data = literal_eval(app.app.GetParameterString("value"))
return data[0] if len(channels) == 1 else data
@@ -126,10 +124,8 @@ class OTBObject(ABC):
"""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
- start = nb_channels + start if isinstance(start,
- int) and start < 0 else start
- stop = nb_channels + stop if isinstance(stop,
- int) and stop < 0 else stop
+ start = nb_channels + start if isinstance(start, int) and start < 0 else start
+ stop = nb_channels + stop if isinstance(stop, int) and stop < 0 else stop
step = 1 if step is None else step
if start is not None and stop is not None:
return list(range(start, stop, step))
@@ -144,7 +140,7 @@ class OTBObject(ABC):
)
def export(
- self, key: str = None, preserve_dtype: bool = True
+ self, key: str = None, preserve_dtype: bool = True
) -> dict[str, dict[str, np.ndarray]]:
"""Export a specific output image as numpy array and store it in object exports_dic.
@@ -162,15 +158,13 @@ class OTBObject(ABC):
if key not in self.exports_dic:
self.exports_dic[key] = self.app.ExportImage(key)
if preserve_dtype:
- self.exports_dic[key]["array"] = self.exports_dic[key][
- "array"].astype(
+ self.exports_dic[key]["array"] = self.exports_dic[key]["array"].astype(
self.dtype
)
return self.exports_dic[key]
def to_numpy(
- self, key: str = None, preserve_dtype: bool = True,
- copy: bool = False
+ self, key: str = None, preserve_dtype: bool = True, copy: bool = False
) -> np.ndarray:
"""Export a pyotb object to numpy array.
@@ -199,8 +193,7 @@ class OTBObject(ABC):
profile = {}
array = self.to_numpy(preserve_dtype=True, copy=False)
proj = self.app.GetImageProjection(self.output_image_key)
- profile.update(
- {"crs": proj, "dtype": array.dtype, "transform": self.transform})
+ profile.update({"crs": proj, "dtype": array.dtype, "transform": self.transform})
height, width, count = array.shape
profile.update({"count": count, "height": height, "width": width})
return np.moveaxis(array, 2, 0), profile
@@ -301,8 +294,7 @@ class OTBObject(ABC):
"""Logical or."""
return self.__create_operator(LogicalOperation, "||", self, other)
- def __and__(self,
- other: OTBObject | str | int | float) -> LogicalOperation:
+ def __and__(self, other: OTBObject | str | int | float) -> LogicalOperation:
"""Logical and."""
return self.__create_operator(LogicalOperation, "&&", self, other)
@@ -398,7 +390,7 @@ class OTBObject(ABC):
return self.get_values_at_coords(row, col, channels)
# Slicing
if not isinstance(key, tuple) or (
- isinstance(key, tuple) and (len(key) < 2 or len(key) > 3)
+ isinstance(key, tuple) and (len(key) < 2 or len(key) > 3)
):
raise ValueError(
f'"{key}" cannot be interpreted as valid slicing. Slicing should be 2D or 3D.'
@@ -454,13 +446,13 @@ class App(OTBObject):
]
def __init__(
- self,
- appname: str,
- *args,
- frozen: bool = False,
- quiet: bool = False,
- name: str = "",
- **kwargs,
+ self,
+ appname: str,
+ *args,
+ frozen: bool = False,
+ quiet: bool = False,
+ name: str = "",
+ **kwargs,
):
"""Common constructor for OTB applications. Handles in-memory connection between apps.
@@ -510,9 +502,8 @@ class App(OTBObject):
self.set_parameters(*args, **kwargs)
# Create Output image objects
for key in filter(
- lambda k: self._out_param_types[
- k] == otb.ParameterType_OutputImage,
- self._out_param_types,
+ lambda k: self._out_param_types[k] == otb.ParameterType_OutputImage,
+ self._out_param_types,
):
self.outputs[key] = Output(self, key, self._settings.get(key))
if not self.frozen:
@@ -533,8 +524,7 @@ class App(OTBObject):
@property
def parameters(self):
"""Return used OTB application parameters."""
- return {**self._auto_parameters, **self.app.GetParameters(),
- **self._settings}
+ return {**self._auto_parameters, **self.app.GetParameters(), **self._settings}
@property
def exports_dic(self) -> dict[str, dict]:
@@ -544,8 +534,7 @@ class App(OTBObject):
def __is_one_of_types(self, key: str, param_types: list[int]) -> bool:
"""Helper to factor is_input and is_output."""
if key not in self._all_param_types:
- raise KeyError(
- f"key {key} not found in the application parameters types")
+ raise KeyError(f"key {key} not found in the application parameters types")
return self._all_param_types[key] in param_types
def is_input(self, key: str) -> bool:
@@ -558,8 +547,7 @@ class App(OTBObject):
True if the parameter is an input, else False
"""
- return self.__is_one_of_types(key=key,
- param_types=self.INPUT_PARAM_TYPES)
+ return self.__is_one_of_types(key=key, param_types=self.INPUT_PARAM_TYPES)
def is_output(self, key: str) -> bool:
"""Returns True if the key is an output.
@@ -571,8 +559,7 @@ class App(OTBObject):
True if the parameter is an output, else False
"""
- return self.__is_one_of_types(key=key,
- param_types=self.OUTPUT_PARAM_TYPES)
+ return self.__is_one_of_types(key=key, param_types=self.OUTPUT_PARAM_TYPES)
def is_key_list(self, key: str) -> bool:
"""Check if a parameter key is an input parameter list."""
@@ -696,8 +683,7 @@ class App(OTBObject):
dtype = get_pixel_type(param)
except (TypeError, RuntimeError):
logger.warning(
- '%s: unable to identify pixel type of key "%s"', self.name,
- param
+ '%s: unable to identify pixel type of key "%s"', self.name, param
)
return
if target_key:
@@ -713,8 +699,7 @@ class App(OTBObject):
def execute(self):
"""Execute and write to disk if any output parameter has been set during init."""
- logger.debug("%s: run execute() with parameters=%s", self.name,
- self.parameters)
+ logger.debug("%s: run execute() with parameters=%s", self.name, self.parameters)
self._time_start = perf_counter()
try:
self.app.Execute()
@@ -742,36 +727,28 @@ class App(OTBObject):
self._time_end = perf_counter()
def write(
- self,
- path: str | Path | dict[str, str] = None,
- pixel_type: dict[str, str] | str = None,
- preserve_dtype: bool = False,
- ext_fname: str | dict[str, str] | dict[str, int] | dict[
- str, float] = None,
- **kwargs,
+ self,
+ path: str | Path | dict[str, str] = None,
+ pixel_type: dict[str, str] | str = None,
+ preserve_dtype: bool = False,
+ ext_fname: str = "",
+ **kwargs,
) -> bool:
"""Set output pixel type and write the output raster files.
Args:
- path: Can be :
- - filepath, useful when there is only one output, e.g.
- 'output.tif'
- - dictionary containing key-arguments enumeration. Useful when
- a key contains non-standard characters such as a point, e.g.
- {'io.out':'output.tif'}
- - None if output file was passed during App init
- ext_fname: Optional, an extended filename as understood by OTB
- (e.g. "&gdal:co:TILED=YES") or a dict of key/value. Will be
- used for all outputs.
- pixel_type: Can be :
- - dictionary {out_param_key: pixeltype} when specifying for
- several outputs
- - str (e.g. 'uint16') or otbApplication.ImagePixelType_...
- When there are several outputs, all outputs are written with
- this unique type. Valid pixel types are uint8, uint16, uint32,
- int16, int32, float, double, cint16, cint32, cfloat, cdouble.
- preserve_dtype: propagate main input pixel type to outputs, in
- case pixel_type is None
+ path: Can be : - filepath, useful when there is only one output, e.g. 'output.tif'
+ - dictionary containing key-arguments enumeration. Useful when a key contains
+ non-standard characters such as a point, e.g. {'io.out':'output.tif'}
+ - None if output file was passed during App init
+ ext_fname: Optional, an extended filename as understood by OTB (e.g. "&gdal:co:TILED=YES")
+ Will be used for all outputs (Default value = "")
+ pixel_type: Can be : - dictionary {out_param_key: pixeltype} when specifying for several outputs
+ - str (e.g. 'uint16') or otbApplication.ImagePixelType_... When there are several
+ outputs, all outputs are written with this unique type.
+ Valid pixel types are uint8, uint16, uint32, int16, int32, float, double,
+ cint16, cint32, cfloat, cdouble. (Default value = None)
+ preserve_dtype: propagate main input pixel type to outputs, in case pixel_type is None
**kwargs: keyword arguments e.g. out='output.tif'
Returns:
@@ -790,10 +767,8 @@ class App(OTBObject):
elif isinstance(path, (str, Path)) and self.output_key:
kwargs.update({self.output_key: str(path)})
elif path is not None:
- raise TypeError(
- f"{self.name}: unsupported filepath type ({type(path)})")
- if not (kwargs or any(
- k in self._settings for k in self._out_param_types)):
+ raise TypeError(f"{self.name}: unsupported filepath type ({type(path)})")
+ if not (kwargs or any(k in self._settings for k in self._out_param_types)):
raise KeyError(
f"{self.name}: at least one filepath is required, if not provided during App init"
)
@@ -837,17 +812,14 @@ class App(OTBObject):
dtype = parse_pixel_type(pixel_type)
type_name = self.app.ConvertPixelTypeToNumpy(dtype)
logger.debug(
- '%s: output(s) will be written with type "%s"', self.name,
- type_name
+ '%s: output(s) will be written with type "%s"', self.name, type_name
)
for key in parameters:
- if self._out_param_types[
- key] == otb.ParameterType_OutputImage:
+ if self._out_param_types[key] == otb.ParameterType_OutputImage:
data_types[key] = dtype
elif isinstance(pixel_type, dict):
data_types = {
- key: parse_pixel_type(dtype) for key, dtype in
- pixel_type.items()
+ key: parse_pixel_type(dtype) for key, dtype in pixel_type.items()
}
elif preserve_dtype:
self.propagate_dtype() # all outputs will have the same type as the main input raster
@@ -880,8 +852,7 @@ class App(OTBObject):
return bool(files) and not missing
# Private functions
- def __parse_args(self, args: list[str | OTBObject | dict | list]) -> dict[
- str, Any]:
+ def __parse_args(self, args: list[str | OTBObject | dict | list]) -> dict[str, Any]:
"""Gather all input arguments in kwargs dict.
Args:
@@ -896,16 +867,15 @@ class App(OTBObject):
if isinstance(arg, dict):
kwargs.update(arg)
elif (
- isinstance(arg, (str, OTBObject))
- or isinstance(arg, list)
- and self.is_key_list(self.input_key)
+ isinstance(arg, (str, OTBObject))
+ or isinstance(arg, list)
+ and self.is_key_list(self.input_key)
):
kwargs.update({self.input_key: arg})
return kwargs
def __set_param(
- self, key: str,
- obj: list | tuple | OTBObject | otb.Application | list[Any]
+ self, key: str, obj: list | tuple | OTBObject | otb.Application | list[Any]
):
"""Set one parameter, decide which otb.Application method to use depending on target object."""
if obj is None or (isinstance(obj, (list, tuple)) and not obj):
@@ -915,11 +885,11 @@ class App(OTBObject):
if isinstance(obj, OTBObject):
self.app.ConnectImage(key, obj.app, obj.output_image_key)
elif isinstance(
- obj, otb.Application
+ obj, otb.Application
): # this is for backward comp with plain OTB
self.app.ConnectImage(key, obj, get_out_images_param_keys(obj)[0])
elif (
- key == "ram"
+ key == "ram"
): # SetParameterValue in OTB<7.4 doesn't work for ram parameter cf gitlab OTB issue 2200
self.app.SetParameterInt("ram", int(obj))
elif not isinstance(obj, list): # any other parameters (str, int...)
@@ -931,10 +901,9 @@ class App(OTBObject):
if isinstance(inp, OTBObject):
self.app.ConnectImage(key, inp.app, inp.output_image_key)
elif isinstance(
- inp, otb.Application
+ inp, otb.Application
): # this is for backward comp with plain OTB
- self.app.ConnectImage(key, obj,
- get_out_images_param_keys(inp)[0])
+ self.app.ConnectImage(key, obj, get_out_images_param_keys(inp)[0])
else: # here `input` should be an image filepath
# Append `input` to the list, do not overwrite any previously set element of the image list
self.app.AddParameterStringList(key, inp)
@@ -949,9 +918,8 @@ class App(OTBObject):
continue
value = self.app.GetParameterValue(key)
# TODO: here we *should* use self.app.IsParameterEnabled, but it seems broken
- if isinstance(value,
- otb.ApplicationProxy) and self.app.HasAutomaticValue(
- key
+ if isinstance(value, otb.ApplicationProxy) and self.app.HasAutomaticValue(
+ key
):
try:
value = str(
@@ -962,8 +930,7 @@ class App(OTBObject):
except RuntimeError:
continue # grouped parameters
# Save static output data (ReadImageInfo, ComputeImageStatistics, etc.)
- elif self.app.GetParameterRole(key) == 1 and bool(
- value) or value == 0:
+ elif self.app.GetParameterRole(key) == 1 and bool(value) or value == 0:
if isinstance(value, str):
try:
value = literal_eval(value)
@@ -972,8 +939,7 @@ class App(OTBObject):
self.data[key] = value
# Special functions
- def __getitem__(self, key: str) -> Any | list[
- int | float] | int | float | Slicer:
+ def __getitem__(self, key: str) -> Any | list[int | float] | int | float | Slicer:
"""This function is called when we use App()[...].
We allow to return attr if key is a parameter, or call OTBObject __getitem__ for pixel values or Slicer
@@ -987,8 +953,7 @@ class App(OTBObject):
return self.outputs[key]
if key in self.parameters:
return self.parameters[key]
- raise KeyError(
- f"{self.name}: unknown or undefined parameter '{key}'")
+ raise KeyError(f"{self.name}: unknown or undefined parameter '{key}'")
raise TypeError(
f"{self.name}: cannot access object item or slice using {type(key)} object"
)
@@ -998,11 +963,11 @@ class Slicer(App):
"""Slicer objects i.e. when we call something like raster[:, :, 2] from Python."""
def __init__(
- self,
- obj: OTBObject,
- rows: slice,
- cols: slice,
- channels: slice | list[int] | int,
+ self,
+ obj: OTBObject,
+ rows: slice,
+ cols: slice,
+ channels: slice | list[int] | int,
):
"""Create a slicer object, that can be used directly for writing or inside a BandMath.
@@ -1069,10 +1034,9 @@ class Slicer(App):
) # subtract 1 to respect python convention
spatial_slicing = True
# These are some attributes when the user simply wants to extract *one* band to be used in an Operation
- if not spatial_slicing and isinstance(channels, list) and len(
- channels) == 1:
+ if not spatial_slicing and isinstance(channels, list) and len(channels) == 1:
self.one_band_sliced = (
- channels[0] + 1
+ channels[0] + 1
) # OTB convention: channels start at 1
self.input = obj
@@ -1103,8 +1067,7 @@ class Operation(App):
"""
- def __init__(self, operator: str, *inputs, nb_bands: int = None,
- name: str = None):
+ def __init__(self, operator: str, *inputs, nb_bands: int = None, name: str = None):
"""Given some inputs and an operator, this function enables to transform this into an OTB application.
Operations generally involve 2 inputs (+, -...). It can have only 1 input for `abs` operator.
@@ -1151,10 +1114,10 @@ class Operation(App):
)
def build_fake_expressions(
- self,
- operator: str,
- inputs: list[OTBObject | str | int | float],
- nb_bands: int = None,
+ self,
+ operator: str,
+ inputs: list[OTBObject | str | int | float],
+ nb_bands: int = None,
):
"""Create a list of 'fake' expressions, one for each band.
@@ -1175,8 +1138,8 @@ class Operation(App):
# For any other operations, the output number of bands is the same as inputs
else:
if any(
- isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
- for inp in inputs
+ isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
+ for inp in inputs
):
nb_bands = 1
else:
@@ -1187,10 +1150,9 @@ class Operation(App):
]
# check that all inputs have the same nb of bands
if len(nb_bands_list) > 1 and not all(
- x == nb_bands_list[0] for x in nb_bands_list
+ x == nb_bands_list[0] for x in nb_bands_list
):
- raise ValueError(
- "All images do not have the same number of bands")
+ raise ValueError("All images do not have the same number of bands")
nb_bands = nb_bands_list[0]
# Create a list of fake expressions, each item of the list corresponding to one band
@@ -1225,7 +1187,7 @@ class Operation(App):
# the false expression stores the expression 2 * str(input1) + str(input2)
fake_exp = f"({expressions[0]} {operator} {expressions[1]})"
elif (
- len(inputs) == 3 and operator == "?"
+ len(inputs) == 3 and operator == "?"
): # this is only for ternary expression
fake_exp = f"({expressions[0]} ? {expressions[1]} : {expressions[2]})"
self.fake_exp_bands.append(fake_exp)
@@ -1247,15 +1209,14 @@ class Operation(App):
one_band_exp = one_band_fake_exp
for inp in self.inputs:
# Replace the name of in-memory object (e.g. '<pyotb.App object>b1' by 'im1b1')
- one_band_exp = one_band_exp.replace(repr(inp),
- self.im_dic[repr(inp)])
+ one_band_exp = one_band_exp.replace(repr(inp), self.im_dic[repr(inp)])
exp_bands.append(one_band_exp)
# Form the final expression (e.g. 'im1b1 + 1; im1b2 + 1')
return exp_bands, ";".join(exp_bands)
@staticmethod
def make_fake_exp(
- x: OTBObject | str, band: int, keep_logical: bool = False
+ x: OTBObject | str, band: int, keep_logical: bool = False
) -> tuple[str, list[OTBObject], int]:
"""This an internal function, only to be used by `build_fake_expressions`.
@@ -1278,8 +1239,7 @@ class Operation(App):
# Special case for one-band slicer
if isinstance(x, Slicer) and hasattr(x, "one_band_sliced"):
if keep_logical and isinstance(x.input, LogicalOperation):
- fake_exp = x.input.logical_fake_exp_bands[
- x.one_band_sliced - 1]
+ fake_exp = x.input.logical_fake_exp_bands[x.one_band_sliced - 1]
inputs, nb_channels = x.input.inputs, x.input.nb_channels
elif isinstance(x.input, Operation):
# Keep only one band of the expression
@@ -1331,17 +1291,16 @@ class LogicalOperation(Operation):
"""
self.logical_fake_exp_bands = []
- super().__init__(operator, *inputs, nb_bands=nb_bands,
- name="LogicalOperation")
+ super().__init__(operator, *inputs, nb_bands=nb_bands, name="LogicalOperation")
self.logical_exp_bands, self.logical_exp = self.get_real_exp(
self.logical_fake_exp_bands
)
def build_fake_expressions(
- self,
- operator: str,
- inputs: list[OTBObject | str | int | float],
- nb_bands: int = None,
+ self,
+ operator: str,
+ inputs: list[OTBObject | str | int | float],
+ nb_bands: int = None,
):
"""Create a list of 'fake' expressions, one for each band.
@@ -1356,8 +1315,8 @@ class LogicalOperation(Operation):
"""
# For any other operations, the output number of bands is the same as inputs
if any(
- isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
- for inp in inputs
+ isinstance(inp, Slicer) and hasattr(inp, "one_band_sliced")
+ for inp in inputs
):
nb_bands = 1
else:
@@ -1368,10 +1327,9 @@ class LogicalOperation(Operation):
]
# check that all inputs have the same nb of bands
if len(nb_bands_list) > 1 and not all(
- x == nb_bands_list[0] for x in nb_bands_list
+ x == nb_bands_list[0] for x in nb_bands_list
):
- raise ValueError(
- "All images do not have the same number of bands")
+ raise ValueError("All images do not have the same number of bands")
nb_bands = nb_bands_list[0]
# Create a list of fake exp, each item of the list corresponding to one band
for i, band in enumerate(range(1, nb_bands + 1)):
@@ -1424,11 +1382,11 @@ class Output(OTBObject):
_filepath: str | Path = None
def __init__(
- self,
- pyotb_app: App,
- param_key: str = None,
- filepath: str = None,
- mkdir: bool = True,
+ self,
+ pyotb_app: App,
+ param_key: str = None,
+ filepath: str = None,
+ mkdir: bool = True,
):
"""Constructor for an Output object.
@@ -1475,8 +1433,7 @@ class Output(OTBObject):
@filepath.setter
def filepath(self, path: str):
if isinstance(path, str):
- if path and not path.startswith(
- ("/vsi", "http://", "https://", "ftp://")):
+ if path and not path.startswith(("/vsi", "http://", "https://", "ftp://")):
path = Path(path.split("?")[0])
self._filepath = path
@@ -1498,8 +1455,7 @@ class Output(OTBObject):
return self.parent_pyotb_app.write(
{self.output_image_key: self.filepath}, **kwargs
)
- return self.parent_pyotb_app.write({self.output_image_key: filepath},
- **kwargs)
+ return self.parent_pyotb_app.write({self.output_image_key: filepath}, **kwargs)
def __str__(self) -> str:
"""Return string representation of Output filepath."""
@@ -1556,13 +1512,12 @@ def get_nbchannels(inp: str | Path | OTBObject) -> int:
info = App("ReadImageInfo", inp, quiet=True)
return info["numberbands"]
except (
- RuntimeError
+ RuntimeError
) as info_err: # this happens when we pass a str that is not a filepath
raise TypeError(
f"Could not get the number of channels file '{inp}' ({info_err})"
) from info_err
- raise TypeError(
- f"Can't read number of channels of type '{type(inp)}' object {inp}")
+ raise TypeError(f"Can't read number of channels of type '{type(inp)}' object {inp}")
def get_pixel_type(inp: str | Path | OTBObject) -> str:
@@ -1583,15 +1538,14 @@ def get_pixel_type(inp: str | Path | OTBObject) -> str:
info = App("ReadImageInfo", inp, quiet=True)
datatype = info["datatype"] # which is such as short, float...
except (
- RuntimeError
+ RuntimeError
) as info_err: # this happens when we pass a str that is not a filepath
raise TypeError(
f"Could not get the pixel type of `{inp}` ({info_err})"
) from info_err
if datatype:
return parse_pixel_type(datatype)
- raise TypeError(
- f"Could not get the pixel type of {type(inp)} object {inp}")
+ raise TypeError(f"Could not get the pixel type of {type(inp)} object {inp}")
def parse_pixel_type(pixel_type: str | int) -> int:
@@ -1621,8 +1575,7 @@ def parse_pixel_type(pixel_type: str | int) -> int:
if pixel_type in datatype_to_pixeltype.values():
return getattr(otb, f"ImagePixelType_{pixel_type}")
if pixel_type in datatype_to_pixeltype:
- return getattr(otb,
- f"ImagePixelType_{datatype_to_pixeltype[pixel_type]}")
+ return getattr(otb, f"ImagePixelType_{datatype_to_pixeltype[pixel_type]}")
raise KeyError(
f"Unknown data type `{pixel_type}`. Available ones: {datatype_to_pixeltype}"
)
@@ -1641,9 +1594,9 @@ def get_out_images_param_keys(app: OTBObject) -> list[str]:
def summarize(
- obj: App | Output | Any,
- strip_input_paths: bool = False,
- strip_output_paths: bool = False,
+ obj: App | Output | Any,
+ strip_input_paths: bool = False,
+ strip_output_paths: bool = False,
) -> dict[str, str | dict[str, Any]]:
"""Recursively summarize parameters of an App or Output object and its parents.
@@ -1677,10 +1630,10 @@ def summarize(
parameters = {}
for key, param in obj.parameters.items():
if (
- strip_input_paths
- and obj.is_input(key)
- or strip_output_paths
- and obj.is_output(key)
+ strip_input_paths
+ and obj.is_input(key)
+ or strip_output_paths
+ and obj.is_output(key)
):
parameters[key] = (
[strip_path(p) for p in param]
--
GitLab
From aa2ae0245b482d3683a9df9080b8d1d804be31af Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 10:36:44 +0200
Subject: [PATCH 07/23] FIX: ext_fname prevail over extensions in filepath
---
pyotb/core.py | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index b776a3d..52b3ffc 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -795,13 +795,14 @@ class App(OTBObject):
for key, filepath in kwargs.items():
if self._out_param_types[key] == otb.ParameterType_OutputImage:
# grab already set extended filename key/values
- already_set_ext = _str2dict(filepath.split("?&")[0]) \
- if "?&" in filepath else {}
+ if "?&" in filepath:
+ filepath, already_set_ext = filepath.split("?&", 1)
+ # ext_fname prevail over extensions in filepath
+ ext_fname = {**_str2dict(already_set_ext), **ext_fname}
# transform dict to str
ext_fname_str = "&".join([
- f"{k}={v}" for k, v in ext_fname.items()
- if k not in already_set_ext
+ f"{key}={value}" for key, value in ext_fname.items()
])
parameters[key] = f"{filepath}?&{ext_fname_str}"
--
GitLab
From 2b526505f832959a0c75c6b0d1cc3dd74fb1446c Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 10:50:08 +0200
Subject: [PATCH 08/23] TEST: strenghten ext_fname tests
---
tests/test_core.py | 26 ++++++++++++++++++++++++++
1 file changed, 26 insertions(+)
diff --git a/tests/test_core.py b/tests/test_core.py
index b19e92b..8d2c1e2 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -111,9 +111,17 @@ def test_write():
def test_ext_fname():
+ def _check(expected: str):
+ fn = INPUT.app.GetParameterString("out")
+ assert "?&" in fn
+ assert fn.split("?&", 1) == expected
+
assert INPUT.write("/tmp/test_write.tif", ext_fname="nodata=0")
+ _check("nodata=0")
assert INPUT.write("/tmp/test_write.tif", ext_fname={"nodata": "0"})
+ _check("nodata=0")
assert INPUT.write("/tmp/test_write.tif", ext_fname={"nodata": 0})
+ _check("nodata=0")
assert INPUT.write(
"/tmp/test_write.tif",
ext_fname={
@@ -121,10 +129,28 @@ def test_ext_fname():
"gdal:co:COMPRESS": "DEFLATE"
}
)
+ _check("nodata=0&gdal:co:COMPRESS=DEFLATE")
assert INPUT.write(
"/tmp/test_write.tif",
ext_fname="nodata=0&gdal:co:COMPRESS=DEFLATE"
)
+ _check("nodata=0&gdal:co:COMPRESS=DEFLATE")
+ assert INPUT.write(
+ "/tmp/test_write.tif?&box=0:0:10:10",
+ ext_fname={
+ "nodata": "0",
+ "gdal:co:COMPRESS": "DEFLATE",
+ "box": "0:0:20:20"
+ }
+ )
+ _check("box=0:0:20:20&nodata=0&gdal:co:COMPRESS=DEFLATE")
+ _check("nodata=0&gdal:co:COMPRESS=DEFLATE")
+ assert INPUT.write(
+ "/tmp/test_write.tif?&box=0:0:10:10",
+ ext_fname="nodata=0&gdal:co:COMPRESS=DEFLATE&box=0:0:20:20"
+ )
+ _check("box=0:0:20:20&nodata=0&gdal:co:COMPRESS=DEFLATE")
+
INPUT["out"].filepath.unlink()
--
GitLab
From 6af96f3d38197a72077c026ed6b815bac8e2f49a Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 11:00:24 +0200
Subject: [PATCH 09/23] TEST: strenghten ext_fname tests
---
tests/test_core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 8d2c1e2..ea18808 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -114,7 +114,7 @@ def test_ext_fname():
def _check(expected: str):
fn = INPUT.app.GetParameterString("out")
assert "?&" in fn
- assert fn.split("?&", 1) == expected
+ assert fn.split("?&", 1)[1] == expected
assert INPUT.write("/tmp/test_write.tif", ext_fname="nodata=0")
_check("nodata=0")
--
GitLab
From 38f320dcbbd5d1dbb80e638cd65a811607b3e502 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Cresson?= <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:06:56 +0000
Subject: [PATCH 10/23] Apply 1 suggestion(s) to 1 file(s)
---
pyotb/core.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 52b3ffc..bddd15c 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -776,7 +776,8 @@ class App(OTBObject):
# Append filename extension to filenames
if ext_fname:
- assert isinstance(ext_fname, (dict, str))
+ if not isinstance(ext_fname, (dict, str)):
+ raise ValueError("Extended filename must be a str or a dict")
def _str2dict(ext_str):
"""Function that converts str to dict."""
return dict(
--
GitLab
From 0fc010c6c3a93dcdadb61f065faded705282b007 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Cresson?= <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:11:42 +0000
Subject: [PATCH 11/23] Apply 1 suggestion(s) to 1 file(s)
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index bddd15c..94faa6b 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -799,7 +799,7 @@ class App(OTBObject):
if "?&" in filepath:
filepath, already_set_ext = filepath.split("?&", 1)
# ext_fname prevail over extensions in filepath
- ext_fname = {**_str2dict(already_set_ext), **ext_fname}
+ ext_fname.update(_str2dict(already_set_ext))
# transform dict to str
ext_fname_str = "&".join([
--
GitLab
From d1cdccfd05853ec8ab3603a179b0624ddccc69f6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Cresson?= <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:12:30 +0000
Subject: [PATCH 12/23] Apply 2 suggestion(s) to 1 file(s)
---
tests/test_core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index ea18808..1a628c2 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -143,13 +143,13 @@ def test_ext_fname():
"box": "0:0:20:20"
}
)
- _check("box=0:0:20:20&nodata=0&gdal:co:COMPRESS=DEFLATE")
+ _check("box=0:0:10:10&nodata=0&gdal:co:COMPRESS=DEFLATE")
_check("nodata=0&gdal:co:COMPRESS=DEFLATE")
assert INPUT.write(
"/tmp/test_write.tif?&box=0:0:10:10",
ext_fname="nodata=0&gdal:co:COMPRESS=DEFLATE&box=0:0:20:20"
)
- _check("box=0:0:20:20&nodata=0&gdal:co:COMPRESS=DEFLATE")
+ _check("box=0:0:10:10&nodata=0&gdal:co:COMPRESS=DEFLATE")
INPUT["out"].filepath.unlink()
--
GitLab
From b80fd7e06c58f1bae1a11b4d11dacb6f5a18a683 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?R=C3=A9mi=20Cresson?= <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 09:12:48 +0000
Subject: [PATCH 13/23] Apply 1 suggestion(s) to 1 file(s)
---
pyotb/core.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 94faa6b..e9319a1 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -780,10 +780,8 @@ class App(OTBObject):
raise ValueError("Extended filename must be a str or a dict")
def _str2dict(ext_str):
"""Function that converts str to dict."""
- return dict(
- keyval for pair in ext_str.split("&")
- if len(keyval := pair.split("=")) == 2
- )
+ splits = [pair.split("=") for pair in ext_str.split("&")]
+ return dict(split for split in splits if len(split) == 2)
if isinstance(ext_fname, str):
# transform str to dict
--
GitLab
From 5bf540388b3f9fe42e16dd8e9462b13006b390a6 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 14:16:24 +0200
Subject: [PATCH 14/23] ADD: fix ext_fname tests
---
tests/test_core.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 1a628c2..824195a 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -143,13 +143,14 @@ def test_ext_fname():
"box": "0:0:20:20"
}
)
- _check("box=0:0:10:10&nodata=0&gdal:co:COMPRESS=DEFLATE")
- _check("nodata=0&gdal:co:COMPRESS=DEFLATE")
+ # Check that the bbox is the one specified in the filepath, not the one
+ # specified in `ext_filename`
+ _check("nodata=0&gdal:co:COMPRESS=DEFLATE&box=0:0:10:10")
assert INPUT.write(
"/tmp/test_write.tif?&box=0:0:10:10",
ext_fname="nodata=0&gdal:co:COMPRESS=DEFLATE&box=0:0:20:20"
)
- _check("box=0:0:10:10&nodata=0&gdal:co:COMPRESS=DEFLATE")
+ _check("nodata=0&gdal:co:COMPRESS=DEFLATE&box=0:0:10:10")
INPUT["out"].filepath.unlink()
--
GitLab
From 5b702ca36a5f4c8fad964269ec4b674025e40ad1 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 14:42:54 +0200
Subject: [PATCH 15/23] FIX: copy ext_fname when it's a dict
---
pyotb/core.py | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index e9319a1..b717acc 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -783,12 +783,11 @@ class App(OTBObject):
splits = [pair.split("=") for pair in ext_str.split("&")]
return dict(split for split in splits if len(split) == 2)
- if isinstance(ext_fname, str):
- # transform str to dict
- ext_fname = _str2dict(ext_fname)
+ new_ext_fname = _str2dict(ext_fname) \
+ if isinstance(ext_fname, str) else ext_fname.copy()
logger.debug("%s: extended filename for outputs:", self.name)
- for key, ext in ext_fname.items():
+ for key, ext in new_ext_fname.items():
logger.debug("%s: %s", key, ext)
for key, filepath in kwargs.items():
@@ -797,11 +796,12 @@ class App(OTBObject):
if "?&" in filepath:
filepath, already_set_ext = filepath.split("?&", 1)
# ext_fname prevail over extensions in filepath
- ext_fname.update(_str2dict(already_set_ext))
+ new_ext_fname.update(_str2dict(already_set_ext))
# transform dict to str
ext_fname_str = "&".join([
- f"{key}={value}" for key, value in ext_fname.items()
+ f"{key}={value}"
+ for key, value in new_ext_fname.items()
])
parameters[key] = f"{filepath}?&{ext_fname_str}"
--
GitLab
From b0122b170ef162b7dfccb0e04d63853582ebc973 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 14:55:23 +0200
Subject: [PATCH 16/23] FIX: copy ext_fname when it's a dict
---
pyotb/core.py | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index b717acc..7e13e91 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -783,11 +783,11 @@ class App(OTBObject):
splits = [pair.split("=") for pair in ext_str.split("&")]
return dict(split for split in splits if len(split) == 2)
- new_ext_fname = _str2dict(ext_fname) \
+ gen_ext_fname = _str2dict(ext_fname) \
if isinstance(ext_fname, str) else ext_fname.copy()
- logger.debug("%s: extended filename for outputs:", self.name)
- for key, ext in new_ext_fname.items():
+ logger.debug("%s: extended filename for all outputs:", self.name)
+ for key, ext in gen_ext_fname.items():
logger.debug("%s: %s", key, ext)
for key, filepath in kwargs.items():
@@ -796,6 +796,7 @@ class App(OTBObject):
if "?&" in filepath:
filepath, already_set_ext = filepath.split("?&", 1)
# ext_fname prevail over extensions in filepath
+ new_ext_fname = gen_ext_fname.copy()
new_ext_fname.update(_str2dict(already_set_ext))
# transform dict to str
--
GitLab
From d953d9578efca316987930430d1580d870c8c055 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 14:57:50 +0200
Subject: [PATCH 17/23] FIX: copy ext_fname when it's a dict
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 7e13e91..a0f4a6f 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -784,7 +784,7 @@ class App(OTBObject):
return dict(split for split in splits if len(split) == 2)
gen_ext_fname = _str2dict(ext_fname) \
- if isinstance(ext_fname, str) else ext_fname.copy()
+ if isinstance(ext_fname, str) else ext_fname
logger.debug("%s: extended filename for all outputs:", self.name)
for key, ext in gen_ext_fname.items():
--
GitLab
From e6f14025dca52271b3e8956e583152dd83a8f69e Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 14:58:28 +0200
Subject: [PATCH 18/23] FIX: copy ext_fname when it's a dict
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index a0f4a6f..206a10f 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -795,7 +795,7 @@ class App(OTBObject):
# grab already set extended filename key/values
if "?&" in filepath:
filepath, already_set_ext = filepath.split("?&", 1)
- # ext_fname prevail over extensions in filepath
+ # extensions in filepath prevail over `new_ext_fname`
new_ext_fname = gen_ext_fname.copy()
new_ext_fname.update(_str2dict(already_set_ext))
--
GitLab
From af0b763c21f4e508e0b882d8bc6da6a8ba63f9b4 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 15:00:15 +0200
Subject: [PATCH 19/23] FIX: copy ext_fname when it's a dict
---
pyotb/core.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 206a10f..9d8ee47 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -792,11 +792,12 @@ class App(OTBObject):
for key, filepath in kwargs.items():
if self._out_param_types[key] == otb.ParameterType_OutputImage:
+ new_ext_fname = gen_ext_fname.copy()
+
# grab already set extended filename key/values
if "?&" in filepath:
filepath, already_set_ext = filepath.split("?&", 1)
# extensions in filepath prevail over `new_ext_fname`
- new_ext_fname = gen_ext_fname.copy()
new_ext_fname.update(_str2dict(already_set_ext))
# transform dict to str
--
GitLab
From 0c2bc2191b1df0e38eb432ad7f518eff4a8ca223 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 15:07:53 +0200
Subject: [PATCH 20/23] ENH: ext_fn tests with 2 outputs
---
tests/test_core.py | 23 +++++++++++++++++++++--
1 file changed, 21 insertions(+), 2 deletions(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 824195a..5955e11 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -111,8 +111,8 @@ def test_write():
def test_ext_fname():
- def _check(expected: str):
- fn = INPUT.app.GetParameterString("out")
+ def _check(expected: str, key: str = "out", app = INPUT.app):
+ fn = app.GetParameterString(key)
assert "?&" in fn
assert fn.split("?&", 1)[1] == expected
@@ -154,6 +154,25 @@ def test_ext_fname():
INPUT["out"].filepath.unlink()
+ mss = pyotb.MeanShiftSmoothing({
+ "in": FILEPATH
+ })
+ mss.write(
+ {
+ "fout": "/tmp/test_ext_fn_fout.tif&?nodata=1",
+ "foutpos": "/tmp/test_ext_fn_foutpos.tif?&nodata=2"
+ },
+ ext_fname={
+ "nodata": 0,
+ "gdal:co:COMPRESS": "DEFLATE"
+ }
+ )
+ _check("nodata=1&gdal:co:COMPRESS=DEFLATE", key="fout", app=mss.app)
+ _check("nodata=2&gdal:co:COMPRESS=DEFLATE", key="foutpos", app=mss.app)
+ mss["fout"].filepath.unlink()
+ mss["foutpos"].filepath.unlink()
+
+
def test_frozen_app_write():
app = pyotb.BandMath(INPUT, exp="im1b1", frozen=True)
--
GitLab
From 1e68f1e0b03b1f1fb5d9592982af8b9f1aeae6ef Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Wed, 28 Jun 2023 15:15:36 +0200
Subject: [PATCH 21/23] ENH: ext_fn tests with 2 outputs
---
tests/test_core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 5955e11..7ca58dd 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -159,7 +159,7 @@ def test_ext_fname():
})
mss.write(
{
- "fout": "/tmp/test_ext_fn_fout.tif&?nodata=1",
+ "fout": "/tmp/test_ext_fn_fout.tif?&nodata=1",
"foutpos": "/tmp/test_ext_fn_foutpos.tif?&nodata=2"
},
ext_fname={
--
GitLab
From 68e7fdb77febe206af7bfe5d6a6211e98fe95c09 Mon Sep 17 00:00:00 2001
From: Vincent Delbar <vincent.delbar@latelescop.fr>
Date: Wed, 28 Jun 2023 13:26:25 +0000
Subject: [PATCH 22/23] Apply 1 suggestion(s) to 1 file(s)
---
pyotb/core.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 9d8ee47..58f3f8f 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -783,16 +783,16 @@ class App(OTBObject):
splits = [pair.split("=") for pair in ext_str.split("&")]
return dict(split for split in splits if len(split) == 2)
- gen_ext_fname = _str2dict(ext_fname) \
- if isinstance(ext_fname, str) else ext_fname
+ if isinstance(ext_fname, str):
+ ext_fname = _str2dict(ext_fname)
logger.debug("%s: extended filename for all outputs:", self.name)
- for key, ext in gen_ext_fname.items():
+ for key, ext in ext_fname.items():
logger.debug("%s: %s", key, ext)
for key, filepath in kwargs.items():
if self._out_param_types[key] == otb.ParameterType_OutputImage:
- new_ext_fname = gen_ext_fname.copy()
+ new_ext_fname = ext_fname.copy()
# grab already set extended filename key/values
if "?&" in filepath:
--
GitLab
From 5f837beff8b51d0d7601ce3f6a57f109537f0716 Mon Sep 17 00:00:00 2001
From: Vincent Delbar <vincent.delbar@latelescop.fr>
Date: Wed, 28 Jun 2023 13:28:14 +0000
Subject: [PATCH 23/23] Apply 1 suggestion(s) to 1 file(s)
---
tests/test_core.py | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/tests/test_core.py b/tests/test_core.py
index 7ca58dd..c3cedef 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -154,9 +154,7 @@ def test_ext_fname():
INPUT["out"].filepath.unlink()
- mss = pyotb.MeanShiftSmoothing({
- "in": FILEPATH
- })
+ mss = pyotb.MeanShiftSmoothing(FILEPATH)
mss.write(
{
"fout": "/tmp/test_ext_fn_fout.tif?&nodata=1",
--
GitLab