From 644654c58c6e7f7ee15766d54c0b98df01be86ae Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Tue, 15 Mar 2022 17:16:50 +0100
Subject: [PATCH 1/3] FIX: only set OTB_TF_NSOURCES if there is a valid source
in args
---
pyotb/apps.py | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/pyotb/apps.py b/pyotb/apps.py
index 243131e..9927c83 100644
--- a/pyotb/apps.py
+++ b/pyotb/apps.py
@@ -108,7 +108,8 @@ for _app in AVAILABLE_APPLICATIONS:
# Retrieving the number of `source#.il` parameters
params_dic = {k: v for arg in args if isinstance(arg, dict) for k, v in arg.items()}
n_sources = len([k for k in params_dic if k.startswith('source') and k.endswith('.il')])
- os.environ['OTB_TF_NSOURCES'] = str(n_sources)
+ if n_sources > 1:
+ os.environ['OTB_TF_NSOURCES'] = str(n_sources)
def __init__(self, *args, n_sources=None, **kwargs):
"""
--
GitLab
From 9d3253440dced68ca7cba0cc2d85cae9c2b51b3b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Nicolas=20Nar=C3=A7on?= <nicolas.narcon@gmail.com>
Date: Tue, 15 Mar 2022 16:24:40 +0000
Subject: [PATCH 2/3] FIX: transform > to >=
---
pyotb/apps.py | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/pyotb/apps.py b/pyotb/apps.py
index 9927c83..9bf6759 100644
--- a/pyotb/apps.py
+++ b/pyotb/apps.py
@@ -108,7 +108,7 @@ for _app in AVAILABLE_APPLICATIONS:
# Retrieving the number of `source#.il` parameters
params_dic = {k: v for arg in args if isinstance(arg, dict) for k, v in arg.items()}
n_sources = len([k for k in params_dic if k.startswith('source') and k.endswith('.il')])
- if n_sources > 1:
+ if n_sources >= 1:
os.environ['OTB_TF_NSOURCES'] = str(n_sources)
def __init__(self, *args, n_sources=None, **kwargs):
--
GitLab
From 4fccbbef4d20dbea1e43434e42ecdd1b3d637300 Mon Sep 17 00:00:00 2001
From: Narcon Nicolas <nicolas.narcon@inrae.fr>
Date: Tue, 15 Mar 2022 17:43:01 +0100
Subject: [PATCH 3/3] DOC: bump version + improve example doc
---
README.md | 17 +++++++++--------
pyotb/__init__.py | 2 +-
setup.py | 2 +-
3 files changed, 11 insertions(+), 10 deletions(-)
diff --git a/README.md b/README.md
index 659880c..e0126e0 100644
--- a/README.md
+++ b/README.md
@@ -9,7 +9,7 @@ Requirements:
pip install pyotb --upgrade
```
-For Python>=3.6, latest version available is pyotb 1.3.1. For Python 3.5, latest version available is pyotb 1.2.2
+For Python>=3.6, latest version available is pyotb 1.3.2. 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.
@@ -293,25 +293,26 @@ between Tensorflow and OTBTF, i.e. `import tensorflow` doesn't work in a script
## Some examples
### Compute the mean of several rasters, taking into account NoData
-Let's consider we have at disposal 73 NDVI rasters and their 73 binary cloud masks (where cloud is 1 and clear pixel is 0), corresponding to 73 dates of a year.
+Let's consider we have at disposal 73 NDVI rasters for a year, where clouds have been masked with NoData (nodata value of -10 000 for example).
-Goal: compute the temporal mean (keeping the spatial dimension) of the NDVIs, excluding cloudy pixels. Piece of code to achieve that:
+Goal: compute the mean across time (keeping the spatial dimension) of the NDVIs, excluding cloudy pixels. Piece of code to achieve that:
```python
import pyotb
-masks = [pyotb.Input(path) for path in mask_paths]
+nodata = -10000
+ndvis = [pyotb.Input(path) for path in ndvi_paths]
# For each pixel location, summing all valid NDVI values
-summed = sum([pyotb.where(mask != 1, ndvi, 0) for mask, ndvi in zip(masks, ndvi_paths)])
+summed = sum([pyotb.where(ndvi != nodata, ndvi, 0) for ndvi in ndvis])
# Printing the generated BandMath expression
-print(summed.exp) # this returns a very long exp: (0 + ((im1b1 != 1) ? im2b1 : 0)) + ((im3b1 != 1) ? im4b1 : 0)) + ... + ((im145b1 != 1) ? im146b1 : 0)))
+print(summed.exp) # this returns a very long exp: "0 + ((im1b1 != -10000) ? im1b1 : 0) + ((im2b1 != -10000) ? im2b1 : 0) + ... + ((im73b1 != -10000) ? im73b1 : 0)"
# For each pixel location, getting the count of valid pixels
-count = sum([pyotb.where(mask == 1, 0, 1) for mask in masks])
+count = sum([pyotb.where(ndvi == nodata, 0, 1) for ndvi in ndvis])
-mean = summed / count # BandMath exp of this is very long: (0 + ((im1b1 != 1) ? im2b1 : 0)) + ... + ((im145b1 != 1) ? im146b1 : 0))) / (0 + ((im1b1 == 1) ? 0 : 1)) + ((im3b1 == 1) ? 0 : 1)) + ... + ((im145b1 == 1) ? 0 : 1)))
+mean = summed / count # BandMath exp of this is very long: "(0 + ((im1b1 != -10000) ? im1b1 : 0) + ... + ((im73b1 != -10000) ? im73b1 : 0)) / (0 + ((im1b1 == -10000) ? 0 : 1) + ... + ((im73b1 == -10000) ? 0 : 1))"
mean.write('ndvi_annual_mean.tif')
```
diff --git a/pyotb/__init__.py b/pyotb/__init__.py
index 8ae8d7d..6dd93f6 100644
--- a/pyotb/__init__.py
+++ b/pyotb/__init__.py
@@ -2,7 +2,7 @@
"""
This module provides convenient python wrapping of otbApplications
"""
-__version__ = "1.3"
+__version__ = "1.3.2"
from .apps import *
from .core import App, Output, Input, get_nbchannels, get_pixel_type
diff --git a/setup.py b/setup.py
index 81f3366..5cdf0d6 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="1.3.1",
+ version="1.3.2",
author="Nicolas Narçon",
author_email="nicolas.narcon@gmail.com",
description="Library to enable easy use of the Orfeo Tool Box (OTB) in Python",
--
GitLab