From 4a0b74628ffa5a897413173c038e06480478627f Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Wed, 23 Feb 2022 11:19:51 +0100
Subject: [PATCH 1/6] FIX: use GetParameterOutputImagePixelType instead of
GetImageBasePixelType
---
pyotb/core.py | 18 ++++++++----------
1 file changed, 8 insertions(+), 10 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index 8465840..ca38e60 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -897,19 +897,17 @@ def get_pixel_type(inp):
# Executing the app, without printing its log
info = App("ReadImageInfo", inp, otb_stdout=False)
datatype = info.GetParameterInt("datatype") # which is such as short, float...
- dataype_to_pixeltype = {
- 'unsigned_char': 'uint8', 'short': 'int16', 'unsigned_short': 'uint16',
- 'int': 'int32', 'unsigned_int': 'uint32', 'long': 'int32', 'ulong': 'uint32',
- 'float': 'float','double': 'double'
- }
+ dataype_to_pixeltype = {'unsigned_char': 'uint8', 'short': 'int16', 'unsigned_short': 'uint16',
+ 'int': 'int32', 'unsigned_int': 'uint32', 'long': 'int32', 'ulong': 'uint32',
+ 'float': 'float', 'double': 'double'}
pixel_type = dataype_to_pixeltype[datatype]
pixel_type = getattr(otb, f'ImagePixelType_{pixel_type}')
- elif isinstance(inp, (Input, Output, Operation)):
- pixel_type = inp.GetImageBasePixelType(inp.output_parameter_key)
+ elif isinstance(inp, (Input, Output, Operation, Slicer)):
+ pixel_type = inp.GetParameterOutputImagePixelType(inp.output_parameter_key)
elif isinstance(inp, App):
- if len(inp.output_parameters_keys) > 1:
- pixel_type = inp.GetImageBasePixelType(inp.output_parameters_keys[0])
+ if len(inp.output_parameters_keys) == 1:
+ pixel_type = inp.GetParameterOutputImagePixelType(inp.output_parameters_keys[0])
else:
- pixel_type = {key: inp.GetImageBasePixelType(key) for key in inp.output_parameters_keys}
+ pixel_type = {key: inp.GetParameterOutputImagePixelType(key) for key in inp.output_parameters_keys}
return pixel_type
--
GitLab
From f3988f40e2faca0b281550109af316a3cbccbdbe Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Wed, 23 Feb 2022 12:09:09 +0100
Subject: [PATCH 2/6] ENH: add the ability to propagate pixel types for App.
Add propagation as default behavior for Slicer and Input
---
pyotb/core.py | 45 ++++++++++++++++++++++++++++++++++-----------
1 file changed, 34 insertions(+), 11 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index ca38e60..d1594ed 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -303,7 +303,7 @@ class Slicer(otbObject):
:param channels:
"""
# Initialize the app that will be used for writing the slicer
- app = App('ExtractROI', {"in": input, 'mode': 'extent'})
+ app = App('ExtractROI', {"in": input, 'mode': 'extent'}, propagate_pixel_type=True)
self.output_parameter_key = 'out'
self.name = 'Slicer'
@@ -363,7 +363,7 @@ class Input(otbObject):
Class for transforming a filepath to pyOTB object
"""
def __init__(self, filepath):
- self.app = App('ExtractROI', filepath).app
+ self.app = App('ExtractROI', filepath, propagate_pixel_type=True).app
self.output_parameter_key = 'out'
self.filepath = filepath
self.name = f'Input from {filepath}'
@@ -412,7 +412,7 @@ class App(otbObject):
# This will only store if app has been excuted, then find_output() is called when accessing the property
self._finished = val
- def __init__(self, appname, *args, execute=True, image_dic=None, otb_stdout=True, **kwargs):
+ def __init__(self, appname, *args, execute=True, image_dic=None, otb_stdout=True, propagate_pixel_type=False, **kwargs):
"""
Enables to run an otb app as a oneliner. Handles in-memory connection between apps
:param appname: name of the app, e.g. 'Smoothing'
@@ -426,6 +426,9 @@ class App(otbObject):
the result of app.ExportImage(). Use it when the app takes a numpy array as input.
See this related issue for why it is necessary to keep reference of object:
https://gitlab.orfeo-toolbox.org/orfeotoolbox/otb/-/issues/1824
+ :param otb_stdout: whether to print logs of the app
+ :param propagate_pixel_type: Propagate the pixel type from inputs to output. If several inputs, the type of an
+ arbitrary input is considered. If several outputs, all will have the same type.
:param kwargs: keyword arguments e.g. il=['input1.tif', App_object2, App_object3.out], out='output.tif'
"""
self.appname = appname
@@ -446,6 +449,8 @@ class App(otbObject):
# Run app, write output if needed, update `finished` property
if execute:
self.execute()
+ if propagate_pixel_type:
+ self.__propagate_pixel_type()
# 'Saving' outputs as attributes, i.e. so that they can be accessed like that: App.out
# Also, thanks to __getitem__ method, the outputs can be accessed as App["out"]. This is useful when the key
# contains reserved characters such as a point eg "io.out"
@@ -587,6 +592,21 @@ class App(otbObject):
else:
self.app.SetParameterValue(param, obj)
+ def __propagate_pixel_type(self):
+ """Propagate the pixel type from inputs to output. If several inputs, the type of an arbitrary input
+ is considered. If several outputs, all outputs will have the same type."""
+ pixel_type = None
+ for param in self.parameters.values():
+ try:
+ pixel_type = get_pixel_type(param)
+ except TypeError:
+ pass
+ if not pixel_type:
+ logger.warning(f"{self.name}: Could not propagate pixel type from inputs to output, " +
+ f"no valid input found")
+ else:
+ for out_key in self.output_parameters_keys:
+ self.app.SetParameterOutputImagePixelType(out_key, pixel_type)
def __with_output(self):
"""Check if App has any output parameter key"""
@@ -890,13 +910,17 @@ def get_pixel_type(inp):
"""
Get the encoding of input image pixels
:param inp: a filepath, or any pyotb object
- :return pixel_type: either a dict of pixel types (in case of an App where there are several outputs)
- format is like `otbApplication.ImagePixelType_uint8'
+ :return pixel_type: format is like `otbApplication.ImagePixelType_uint8'. For an App with several outputs, only the
+ pixel type of the first output is returned
+
"""
if isinstance(inp, str):
# Executing the app, without printing its log
- info = App("ReadImageInfo", inp, otb_stdout=False)
- datatype = info.GetParameterInt("datatype") # which is such as short, float...
+ try:
+ info = App("ReadImageInfo", inp, otb_stdout=False)
+ except Exception: # 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')
+ datatype = info.GetParameterString("datatype") # which is such as short, float...
dataype_to_pixeltype = {'unsigned_char': 'uint8', 'short': 'int16', 'unsigned_short': 'uint16',
'int': 'int32', 'unsigned_int': 'uint32', 'long': 'int32', 'ulong': 'uint32',
'float': 'float', 'double': 'double'}
@@ -905,9 +929,8 @@ def get_pixel_type(inp):
elif isinstance(inp, (Input, Output, Operation, Slicer)):
pixel_type = inp.GetParameterOutputImagePixelType(inp.output_parameter_key)
elif isinstance(inp, App):
- if len(inp.output_parameters_keys) == 1:
- pixel_type = inp.GetParameterOutputImagePixelType(inp.output_parameters_keys[0])
- else:
- pixel_type = {key: inp.GetParameterOutputImagePixelType(key) for key in inp.output_parameters_keys}
+ pixel_type = inp.GetParameterOutputImagePixelType(inp.output_parameters_keys[0])
+ else:
+ raise TypeError(f'Could not get the pixel type. Not supported type: {inp}')
return pixel_type
--
GitLab
From b0893edb68e2e85d991bd59c141bd39ba15ddcef Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Wed, 23 Feb 2022 12:11:26 +0100
Subject: [PATCH 3/6] ENH: invert rows and columns in Slicer to follow the
convention obj[x, y]
---
pyotb/core.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index d1594ed..d36f02a 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -114,7 +114,7 @@ class otbObject(ABC):
elif isinstance(key, tuple) and len(key) == 2:
# adding a 3rd dimension
key = key + (slice(None, None, None),)
- (rows, cols, channels) = key
+ (cols, rows, channels) = key
return Slicer(self, rows, cols, channels)
def __getattr__(self, name):
--
GitLab
From 877f169555f6e603c3d7417131bcc591b154ff00 Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Wed, 23 Feb 2022 14:29:10 +0100
Subject: [PATCH 4/6] ENH: enable propagate pixel type for numpy export FIX:
return a copy of the array when running np.asarray to avoid some segfault
---
pyotb/core.py | 22 +++++++++++++++++++---
1 file changed, 19 insertions(+), 3 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index d36f02a..ebe60e7 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -231,16 +231,32 @@ class otbObject(ABC):
def __hash__(self):
return id(self)
- def __array__(self):
+ def to_numpy(self, propagate_pixel_type=False):
"""
- This is called when running np.asarray(pyotb_object)
+ Export a pyotb object to numpy array
:return: a numpy array
"""
if hasattr(self, 'output_parameter_key'): # this is for Input, Output, Operation, Slicer
output_parameter_key = self.output_parameter_key
else: # this is for App
output_parameter_key = self.output_parameters_keys[0]
- return self.app.ExportImage(output_parameter_key)['array']
+
+ array = self.app.ExportImage(output_parameter_key)['array']
+ if propagate_pixel_type:
+ otb_pixeltype = get_pixel_type(self)
+ otb_pixeltype_to_np_pixeltype = {0: np.uint8, 1: np.int16, 2: np.uint16, 3: np.int32, 4: np.uint32,
+ 5: np.float32, 6: np.float64}
+ np_pixeltype = otb_pixeltype_to_np_pixeltype[otb_pixeltype]
+ array = array.astype(np_pixeltype)
+ return array.copy()
+
+ def __array__(self):
+ """
+ This is called when running np.asarray(pyotb_object)
+ :return: a numpy array
+ """
+
+ return self.to_numpy()
def __array_ufunc__(self, ufunc, method, *inputs, **kwargs):
"""
--
GitLab
From 645f327c176ae188d2eafa6fbde01126b9dfa2f6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20Nar=C3=A7on?= <nicolas.narcon@gmail.com>
Date: Thu, 24 Feb 2022 08:34:52 +0000
Subject: [PATCH 5/6] REFAC: comment & move code
---
pyotb/core.py | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/pyotb/core.py b/pyotb/core.py
index ebe60e7..cb74243 100644
--- a/pyotb/core.py
+++ b/pyotb/core.py
@@ -240,15 +240,15 @@ class otbObject(ABC):
output_parameter_key = self.output_parameter_key
else: # this is for App
output_parameter_key = self.output_parameters_keys[0]
-
- array = self.app.ExportImage(output_parameter_key)['array']
+ # we make a copy to avoid some segfault if the reference to app is lost
+ array = self.app.ExportImage(output_parameter_key)['array'].copy()
if propagate_pixel_type:
otb_pixeltype = get_pixel_type(self)
otb_pixeltype_to_np_pixeltype = {0: np.uint8, 1: np.int16, 2: np.uint16, 3: np.int32, 4: np.uint32,
5: np.float32, 6: np.float64}
np_pixeltype = otb_pixeltype_to_np_pixeltype[otb_pixeltype]
array = array.astype(np_pixeltype)
- return array.copy()
+ return array
def __array__(self):
"""
--
GitLab
From 68a19b5a6198552f20d29ba4869f49107deadceb Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Thu, 24 Feb 2022 09:44:39 +0100
Subject: [PATCH 6/6] bump version
---
README.md | 2 +-
pyotb/__init__.py | 2 +-
setup.py | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/README.md b/README.md
index 60aeaba..8f94e4e 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ Requirements:
pip install pyotb
```
-For Python>=3.6, latest version available is pyotb 1.2.3. For Python 3.5, latest version available is pyotb 1.2.2
+For Python>=3.6, latest version available is pyotb 1.3. For Python 3.5, latest version available is pyotb 1.2.2
## Quickstart: running an OTB app as a oneliner
pyotb has been written so that it is more convenient to run an application in Python.
diff --git a/pyotb/__init__.py b/pyotb/__init__.py
index 91fbcf5..8a29946 100644
--- a/pyotb/__init__.py
+++ b/pyotb/__init__.py
@@ -1,5 +1,5 @@
# -*- coding: utf-8 -*-
-__version__ = "1.2.3"
+__version__ = "1.3"
from .apps import *
from .core import App, Output, Input, get_nbchannels, get_pixel_type
diff --git a/setup.py b/setup.py
index b0762e5..5c78ce9 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@ with open("README.md", "r", encoding="utf-8") as fh:
setuptools.setup(
name="pyotb",
- version="1.2.3",
+ version="1.3",
author="Nicolas Narçon",
author_email="nicolas.narcon@gmail.com",
description="Library to enable easy use of the Orfeo Tool Box (OTB) in Python",
--
GitLab