From f7e7fe337aece6fa2b17b77d62df968e5537ffd7 Mon Sep 17 00:00:00 2001
From: Pranjal Dhole <pranjal.dhole@dzne.de>
Date: Tue, 26 Oct 2021 16:05:51 +0200
Subject: [PATCH 1/2] upgrading h5py version to recent since needed by
tensorflow
---
.gitignore | 2 ++
setup.py | 4 ++--
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/.gitignore b/.gitignore
index e013bd8..ddfab69 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,6 @@
+# Auxiliary directories
.cache/
+.vscode/
# compiled python files
*.pyc
diff --git a/setup.py b/setup.py
index 5e77a19..eb8a614 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
from setuptools import setup, find_packages
-reqs = ['h5py==2.10.0',
+reqs = ['h5py>=2.10.0',
'numpy>=1.12.1',
'docopt>=0.6.2',
'tifffile']
@@ -14,7 +14,7 @@ def readme():
setup(name='pyilastik',
- version='0.0.9',
+ version='0.1.0',
description='Read ilastik labels in python',
author='Manuel Schoelling, Christoph Moehl',
author_email='manuel.schoelling@dzne.de, christoph.oliver.moehl@gmail.com',
From 54b5b05bb9ee9cd882ac39860e7ffbf18bbad193 Mon Sep 17 00:00:00 2001
From: Pranjal Dhole <pranjal.dhole@dzne.de>
Date: Tue, 26 Oct 2021 16:30:52 +0200
Subject: [PATCH 2/2] decoding utf-8 object is no longer required, all strings
are unicode objects
---
pyilastik/ilastik_storage_version_01.py | 10 +++++-----
pyilastik/ilastik_version_05.py | 2 +-
pyilastik/lib.py | 2 +-
3 files changed, 7 insertions(+), 7 deletions(-)
diff --git a/pyilastik/ilastik_storage_version_01.py b/pyilastik/ilastik_storage_version_01.py
index d9bad55..05d7505 100644
--- a/pyilastik/ilastik_storage_version_01.py
+++ b/pyilastik/ilastik_storage_version_01.py
@@ -117,14 +117,14 @@ def __init__(self, h5_handle, image_path=None, prediction=False,
self.skip_image = skip_image
try:
- version = self.f.get('/Input Data/StorageVersion')[()].decode()
+ version = self.f.get('/Input Data/StorageVersion')[()]
except AttributeError:
# for ilastik release > 1.3.0
version = self.f.get('/Input Data/StorageVersion')[()]
assert version == '0.2'
def ilastik_version(self):
- version_str = self.f.get('ilastikVersion')[()].decode()
+ version_str = self.f.get('ilastikVersion')[()]
return int(version_str.replace('.', '')[:3])
def __iter__(self):
@@ -164,7 +164,7 @@ def image_path_list(self):
path = self.f.get(
'/Input Data/infos/{lane}/Raw Data/filePath'.format(lane=lane))
- path = path[()].decode()
+ path = path[()]
path_list.append(path)
@@ -184,7 +184,7 @@ def __getitem__(self, i):
lane = 'lane{:04}'.format(i)
path = f.get(
'/Input Data/infos/{lane}/Raw Data/filePath'.format(lane=lane))
- path = path[()].decode()
+ path = path[()]
original_path = path
prediction = None # TODO
@@ -419,7 +419,7 @@ def _get_block_slices(self, item_index):
slice_list = []
for block in self._get_blocks(item_index):
slices = re.findall('([0-9]+):([0-9]+)',
- block.attrs['blockSlice'].decode('ascii'))
+ block.attrs['blockSlice'])
slice_list.append(slices)
return np.array(slice_list).astype('int')
diff --git a/pyilastik/ilastik_version_05.py b/pyilastik/ilastik_version_05.py
index 6dd4188..644dad2 100644
--- a/pyilastik/ilastik_version_05.py
+++ b/pyilastik/ilastik_version_05.py
@@ -21,7 +21,7 @@ def __getitem__(self, i):
f = self.f
dset = f.get('/DataSets/dataItem{:02}'.format(i))
- path = utils.basename(dset.attrs['fileName'].decode('ascii'))
+ path = utils.basename(dset.attrs['fileName'])
img = np.array(dset.get('data')) if not self.skip_image else None
labels = np.array(dset.get('labels/data'))
diff --git a/pyilastik/lib.py b/pyilastik/lib.py
index 9a77e7e..1d86627 100644
--- a/pyilastik/lib.py
+++ b/pyilastik/lib.py
@@ -18,7 +18,7 @@ def read_project(ilastik_file, image_path=None, prediction=False,
version = f.get('/PixelClassification/StorageVersion')
if version is not None:
try:
- version = version[()].decode()
+ version = version[()]
except AttributeError:
# for ilastik releases >1.3.0
version = version[()]