From 4c3c72961a4f3cc53acba9fde70779c1b6b8ab00 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 21:14:51 +0100
Subject: [PATCH 01/11] FIX: summarize() for RasterInterface
---
pyotb/core.py | 51 ++++++++++++++++++++++++++-------------------------
1 file changed, 26 insertions(+), 25 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 3705961..bdf4eb5 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -338,6 +338,22 @@ class ImageObject(ABC):
return pyotb_app
return NotImplemented
+ def summarize(self) -> dict[str, str | dict[str, Any]]:
+ """Serialize an object and its pipeline into a dictionary.
+
+ Returns:
+ nested dictionary summarizing the pipeline
+
+ """
+ parameters = self.parameters.copy()
+ for key, param in parameters.items():
+ # In the following, we replace each parameter which is an ImageObject, with its summary.
+ if isinstance(param, ImageObject): # single parameter
+ parameters[key] = param.summarize()
+ elif isinstance(param, list): # parameter list
+ parameters[key] = [p.summarize() if isinstance(p, ImageObject) else p for p in param]
+ return {"name": self.app.GetName(), "parameters": parameters}
+
class App(ImageObject):
"""Base class that gathers common operations for any OTB application."""
@@ -465,7 +481,7 @@ class App(ImageObject):
except (RuntimeError, TypeError, ValueError, KeyError) as e:
raise RuntimeError(
f"{self.name}: something went wrong before execution "
- f"(while setting parameter '{key}' to '{obj}')"
+ f"(while setting parameter '{key}' to '{obj}': {e})"
) from e
# Update _parameters using values from OtbApplication object
otb_params = self.app.GetParameters().items()
@@ -536,7 +552,7 @@ class App(ImageObject):
try:
self.app.Execute()
except (RuntimeError, FileNotFoundError) as e:
- raise RuntimeError(f"{self.name}: error during during app execution") from e
+ raise RuntimeError(f"{self.name}: error during during app execution ({e}") from e
self.frozen = False
self._time_end = perf_counter()
logger.debug("%s: execution ended", self.name)
@@ -628,22 +644,6 @@ class App(ImageObject):
logger.error("%s: execution seems to have failed, %s does not exist", self.name, filename)
return tuple(files)
- def summarize(self) -> dict[str, str | dict[str, Any]]:
- """Serialize an object and its pipeline into a dictionary.
-
- Returns:
- nested dictionary summarizing the pipeline
-
- """
- parameters = self.parameters.copy()
- for key, param in parameters.items():
- # In the following, we replace each parameter which is an ImageObject, with its summary.
- if isinstance(param, ImageObject): # single parameter
- parameters[key] = param.summarize()
- elif isinstance(param, list): # parameter list
- parameters[key] = [p.summarize() if isinstance(p, ImageObject) else p for p in param]
- return {"name": self.app.GetName(), "parameters": parameters}
-
# Private functions
def __parse_args(self, args: list[str | ImageObject | dict | list]) -> dict[str, Any]:
"""Gather all input arguments in kwargs dict.
@@ -1079,16 +1079,16 @@ class LogicalOperation(Operation):
class Input(App):
"""Class for transforming a filepath to pyOTB object."""
- def __init__(self, path: str):
+ def __init__(self, filepath: str):
"""Default constructor.
Args:
- path: Anything supported by GDAL (local file on the filesystem, remote resource e.g. /vsicurl/.., etc.)
+ filepath: Anything supported by GDAL (local file on the filesystem, remote resource e.g. /vsicurl/.., etc.)
"""
- super().__init__("ExtractROI", {"in": path}, frozen=True)
- self.name = f"Input from {path}"
- self.filepath = Path(path)
+ super().__init__("ExtractROI", {"in": filepath}, frozen=True)
+ self.name = f"Input from {filepath}"
+ self.filepath = Path(filepath)
self.propagate_dtype()
self.execute()
@@ -1112,6 +1112,7 @@ class Output(ImageObject):
"""
self.name = f"Output {param_key} from {pyotb_app.name}"
self.parent_pyotb_app = pyotb_app # keep trace of parent app
+ self.parameters = pyotb_app.parameters
self.app = pyotb_app.app
self.exports_dic = pyotb_app.exports_dic
self.param_key = param_key
@@ -1169,7 +1170,7 @@ def get_nbchannels(inp: str | ImageObject) -> int:
info = App("ReadImageInfo", inp, quiet=True)
nb_channels = info.app.GetParameterInt("numberbands")
except Exception as e: # this happens when we pass a str that is not a filepath
- raise TypeError(f"Could not get the number of channels of '{inp}'. Not a filepath or wrong filepath") from e
+ raise TypeError(f"Could not get the number of channels of '{inp}' ({e})") from e
return nb_channels
@@ -1188,7 +1189,7 @@ def get_pixel_type(inp: str | ImageObject) -> str:
try:
info = App("ReadImageInfo", inp, quiet=True)
except Exception 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}`. Not a filepath or wrong filepath") from info_err
+ raise TypeError(f"Could not get the pixel type of `{inp}` ({info_err})") from info_err
datatype = info.app.GetParameterString("datatype") # which is such as short, float...
if not datatype:
raise TypeError(f"Unable to read pixel type of image {inp}")
--
GitLab
From d6de016596440d1facb081b2fa9b8059199456cd Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 22:05:16 +0100
Subject: [PATCH 02/11] ADD: parameters property to RasterInterface
---
pyotb/core.py | 17 ++++++++++++++---
1 file changed, 14 insertions(+), 3 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index bdf4eb5..37a56bc 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -354,6 +354,10 @@ class ImageObject(ABC):
parameters[key] = [p.summarize() if isinstance(p, ImageObject) else p for p in param]
return {"name": self.app.GetName(), "parameters": parameters}
+ @abstractmethod
+ def parameters(self):
+ """Parameters"""
+
class App(ImageObject):
"""Base class that gathers common operations for any OTB application."""
@@ -385,7 +389,7 @@ class App(ImageObject):
self.image_dic = image_dic
self._time_start, self._time_end = 0, 0
self.exports_dic = {}
- self.parameters = {}
+ self._parameters = {}
# Initialize app, set parameters and execute if not frozen
create = otb.Registry.CreateApplicationWithoutLogger if quiet else otb.Registry.CreateApplication
self.app = create(name)
@@ -446,6 +450,10 @@ class App(ImageObject):
data_dict[str(key)] = value
return data_dict
+ @property
+ def parameters(self):
+ return self._parameters
+
def set_parameters(self, *args, **kwargs):
"""Set some parameters of the app.
@@ -487,7 +495,7 @@ class App(ImageObject):
otb_params = self.app.GetParameters().items()
otb_params = {k: str(v) if isinstance(v, otb.ApplicationProxy) else v for k, v in otb_params}
# Update param dict and save values as object attributes
- self.parameters.update({**parameters, **otb_params})
+ self._parameters.update({**parameters, **otb_params})
self.save_objects()
def propagate_dtype(self, target_key: str = None, dtype: int = None):
@@ -1112,7 +1120,6 @@ class Output(ImageObject):
"""
self.name = f"Output {param_key} from {pyotb_app.name}"
self.parent_pyotb_app = pyotb_app # keep trace of parent app
- self.parameters = pyotb_app.parameters
self.app = pyotb_app.app
self.exports_dic = pyotb_app.exports_dic
self.param_key = param_key
@@ -1129,6 +1136,10 @@ class Output(ImageObject):
"""Force the right key to be used when accessing the ImageObject."""
return self.param_key
+ @property
+ def parameters(self):
+ return self.parent_pyotb_app.parameters
+
def exists(self) -> bool:
"""Check file exist."""
if self.filepath is None:
--
GitLab
From ff71b801656f56db1f7976f34a98f066c7c0f71d Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 22:15:09 +0100
Subject: [PATCH 03/11] ADD: new test to prevent bug
---
tests/test_core.py | 11 +++++++++++
1 file changed, 11 insertions(+)
diff --git a/tests/test_core.py b/tests/test_core.py
index 58ddeac..7bed905 100644
--- a/tests/test_core.py
+++ b/tests/test_core.py
@@ -166,3 +166,14 @@ def test_ndvi_comparison():
thresholded_bandmath = pyotb.where(ndvi_bandmath >= 0.3, 1, 0)
assert thresholded_bandmath.exp == "((((im1b4 - im1b1) / (im1b4 + im1b1)) >= 0.3) ? 1 : 0)"
+
+
+def test_output_in_arg():
+ o = pyotb.Output(INPUT, "out")
+ t = pyotb.ReadImageInfo(o)
+ assert t
+
+
+def test_output_summary():
+ o = pyotb.Output(INPUT, "out")
+ assert o.summarize()
--
GitLab
From c329fc1bed3a92f25132ada7202e7d07d3d45e81 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 22:15:23 +0100
Subject: [PATCH 04/11] STYLE: linter
---
pyotb/core.py | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 37a56bc..b6e6228 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -356,7 +356,7 @@ class ImageObject(ABC):
@abstractmethod
def parameters(self):
- """Parameters"""
+ """Parameters."""
class App(ImageObject):
@@ -452,6 +452,7 @@ class App(ImageObject):
@property
def parameters(self):
+ """Parameters."""
return self._parameters
def set_parameters(self, *args, **kwargs):
@@ -1138,6 +1139,7 @@ class Output(ImageObject):
@property
def parameters(self):
+ """Parameters."""
return self.parent_pyotb_app.parameters
def exists(self) -> bool:
--
GitLab
From 83c1d7a0db7b6aafbafe6421e5c389bf058f08bb Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 22:16:53 +0100
Subject: [PATCH 05/11] REFAC: parameters abstract property in RasterInterface
---
pyotb/core.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/pyotb/core.py b/pyotb/core.py
index b6e6228..3a969f1 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -355,6 +355,7 @@ class ImageObject(ABC):
return {"name": self.app.GetName(), "parameters": parameters}
@abstractmethod
+ @property
def parameters(self):
"""Parameters."""
--
GitLab
From 3ab4fe2c0dc09e8b35fd7cb7e45394f4e4c71a63 Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Thu, 2 Feb 2023 22:26:09 +0100
Subject: [PATCH 06/11] REFAC: parameters abstract property in RasterInterface
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 3a969f1..e363caf 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -354,8 +354,8 @@ class ImageObject(ABC):
parameters[key] = [p.summarize() if isinstance(p, ImageObject) else p for p in param]
return {"name": self.app.GetName(), "parameters": parameters}
- @abstractmethod
@property
+ @abstractmethod
def parameters(self):
"""Parameters."""
--
GitLab
From 5083e62f2a89f00b6e8b015916db1b3b6cb6e64f Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Fri, 3 Feb 2023 13:11:10 +0100
Subject: [PATCH 07/11] ADD: name in RasterInterface
---
pyotb/core.py | 1 +
1 file changed, 1 insertion(+)
diff --git a/pyotb/core.py b/pyotb/core.py
index e363caf..f035979 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -17,6 +17,7 @@ from .helpers import logger
class ImageObject(ABC):
"""Abstraction of an image object."""
+ name: str
app: otb.Application
exports_dic: dict
--
GitLab
From 733e032c4b3a2ba31c1a9ee0c338c219fc82a5ae Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Fri, 3 Feb 2023 13:35:29 +0100
Subject: [PATCH 08/11] REFAC: add parameters as attribute rather than property
---
pyotb/core.py | 24 ++++++------------------
1 file changed, 6 insertions(+), 18 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index f035979..01f1a91 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -19,6 +19,7 @@ class ImageObject(ABC):
name: str
app: otb.Application
+ parameters: dict
exports_dic: dict
@property
@@ -355,10 +356,6 @@ class ImageObject(ABC):
parameters[key] = [p.summarize() if isinstance(p, ImageObject) else p for p in param]
return {"name": self.app.GetName(), "parameters": parameters}
- @property
- @abstractmethod
- def parameters(self):
- """Parameters."""
class App(ImageObject):
@@ -391,7 +388,7 @@ class App(ImageObject):
self.image_dic = image_dic
self._time_start, self._time_end = 0, 0
self.exports_dic = {}
- self._parameters = {}
+ self.parameters = {}
# Initialize app, set parameters and execute if not frozen
create = otb.Registry.CreateApplicationWithoutLogger if quiet else otb.Registry.CreateApplication
self.app = create(name)
@@ -422,7 +419,7 @@ class App(ImageObject):
@property
def key_input_image(self) -> str:
- """Get the name of first input image parameter."""
+ """Name of the first input image parameter."""
return self.get_first_key(param_types=[otb.ParameterType_InputImage, otb.ParameterType_InputImageList])
@property
@@ -452,11 +449,6 @@ class App(ImageObject):
data_dict[str(key)] = value
return data_dict
- @property
- def parameters(self):
- """Parameters."""
- return self._parameters
-
def set_parameters(self, *args, **kwargs):
"""Set some parameters of the app.
@@ -498,7 +490,7 @@ class App(ImageObject):
otb_params = self.app.GetParameters().items()
otb_params = {k: str(v) if isinstance(v, otb.ApplicationProxy) else v for k, v in otb_params}
# Update param dict and save values as object attributes
- self._parameters.update({**parameters, **otb_params})
+ self.parameters.update({**parameters, **otb_params})
self.save_objects()
def propagate_dtype(self, target_key: str = None, dtype: int = None):
@@ -844,7 +836,7 @@ 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):
"""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.
@@ -1126,6 +1118,7 @@ class Output(ImageObject):
self.app = pyotb_app.app
self.exports_dic = pyotb_app.exports_dic
self.param_key = param_key
+ self.parameters = self.parent_pyotb_app.parameters
self.filepath = None
if filepath:
if "?" in filepath:
@@ -1139,11 +1132,6 @@ class Output(ImageObject):
"""Force the right key to be used when accessing the ImageObject."""
return self.param_key
- @property
- def parameters(self):
- """Parameters."""
- return self.parent_pyotb_app.parameters
-
def exists(self) -> bool:
"""Check file exist."""
if self.filepath is None:
--
GitLab
From 683b75cfa40b48ed6ef5fd5af68f9008102a68ee Mon Sep 17 00:00:00 2001
From: Remi Cresson <remi.cresson@inrae.fr>
Date: Fri, 3 Feb 2023 13:46:33 +0100
Subject: [PATCH 09/11] FIX: sync with renamed attrs/cls
---
pyotb/core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 01f1a91..a174e9c 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -836,7 +836,7 @@ class Operation(App):
"""
- def __init__(self, operator: str, *inputs, nb_bands: int = 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.
@@ -874,7 +874,7 @@ class Operation(App):
appname = "BandMath" if len(self.exp_bands) == 1 else "BandMathX"
# Execute app
super().__init__(appname, il=self.unique_inputs, exp=self.exp, quiet=True)
- self.name = f'Operation exp="{self.exp}"'
+ self.name = name or f'Operation exp="{self.exp}"'
def build_fake_expressions(self, operator: str, inputs: list[ImageObject | str | int | float],
nb_bands: int = None):
--
GitLab
From bb9ce48bf66c7476c4d6d78081803396c462d49a Mon Sep 17 00:00:00 2001
From: Vincent Delbar <vincent.delbar@latelescop.fr>
Date: Fri, 3 Feb 2023 17:32:55 +0000
Subject: [PATCH 10/11] BUG: App init error will raise RuntimeError
---
pyotb/core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index a174e9c..319dc64 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -1172,7 +1172,7 @@ def get_nbchannels(inp: str | ImageObject) -> int:
try:
info = App("ReadImageInfo", inp, quiet=True)
nb_channels = info.app.GetParameterInt("numberbands")
- except Exception as e: # this happens when we pass a str that is not a filepath
+ except RuntimeError as e: # this happens when we pass a str that is not a filepath
raise TypeError(f"Could not get the number of channels of '{inp}' ({e})") from e
return nb_channels
@@ -1191,7 +1191,7 @@ def get_pixel_type(inp: str | ImageObject) -> str:
if isinstance(inp, str):
try:
info = App("ReadImageInfo", inp, quiet=True)
- except Exception as info_err: # this happens when we pass a str that is not a filepath
+ except 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
datatype = info.app.GetParameterString("datatype") # which is such as short, float...
if not datatype:
--
GitLab
From 819c3bf681abd096872f16f7803c9c5a92a4a5cb Mon Sep 17 00:00:00 2001
From: Vincent Delbar <vincent.delbar@latelescop.fr>
Date: Fri, 3 Feb 2023 17:34:53 +0000
Subject: [PATCH 11/11] ENH: rename error e to info_err
---
pyotb/core.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 319dc64..b9fa376 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -1172,8 +1172,8 @@ def get_nbchannels(inp: str | ImageObject) -> int:
try:
info = App("ReadImageInfo", inp, quiet=True)
nb_channels = info.app.GetParameterInt("numberbands")
- except RuntimeError as e: # this happens when we pass a str that is not a filepath
- raise TypeError(f"Could not get the number of channels of '{inp}' ({e})") from e
+ except 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 of '{inp}' ({info_err})") from info_err
return nb_channels
--
GitLab