From f220515eb6fa438f45c432530290c8b840e150ff Mon Sep 17 00:00:00 2001
From: Lorenzo ZOLFANELLI <lorenzo.zolfanelli@espci.psl.eu>
Date: Mon, 28 Mar 2022 16:17:49 +0200
Subject: [PATCH] complete fork: nd2reader -> nd2reader2

---
 nd2reader/__init__.py                         |  5 ---
 nd2reader2/__init__.py                        |  5 +++
 {nd2reader => nd2reader2}/artificial.py       |  2 +-
 {nd2reader => nd2reader2}/common.py           | 31 ++++++++++++-------
 .../common_raw_metadata.py                    |  2 +-
 {nd2reader => nd2reader2}/exceptions.py       |  0
 {nd2reader => nd2reader2}/label_map.py        |  0
 {nd2reader => nd2reader2}/legacy.py           |  2 +-
 {nd2reader => nd2reader2}/parser.py           |  8 ++---
 {nd2reader => nd2reader2}/raw_metadata.py     |  4 +--
 {nd2reader => nd2reader2}/reader.py           |  4 +--
 {nd2reader => nd2reader2}/stitched.py         |  0
 setup.py                                      | 14 ++++-----
 test.py                                       |  2 +-
 tests/test_artificial.py                      |  6 ++--
 tests/test_common.py                          |  6 ++--
 tests/test_label_map.py                       |  4 +--
 tests/test_legacy.py                          |  6 ++--
 tests/test_parser.py                          |  6 ++--
 tests/test_raw_metadata.py                    |  8 ++---
 tests/test_reader.py                          |  8 ++---
 tests/test_version.py                         |  2 +-
 22 files changed, 66 insertions(+), 59 deletions(-)
 delete mode 100644 nd2reader/__init__.py
 create mode 100644 nd2reader2/__init__.py
 rename {nd2reader => nd2reader2}/artificial.py (99%)
 rename {nd2reader => nd2reader2}/common.py (90%)
 rename {nd2reader => nd2reader2}/common_raw_metadata.py (98%)
 rename {nd2reader => nd2reader2}/exceptions.py (100%)
 rename {nd2reader => nd2reader2}/label_map.py (100%)
 rename {nd2reader => nd2reader2}/legacy.py (99%)
 rename {nd2reader => nd2reader2}/parser.py (98%)
 rename {nd2reader => nd2reader2}/raw_metadata.py (98%)
 rename {nd2reader => nd2reader2}/reader.py (98%)
 rename {nd2reader => nd2reader2}/stitched.py (100%)

diff --git a/nd2reader/__init__.py b/nd2reader/__init__.py
deleted file mode 100644
index 8354a47..0000000
--- a/nd2reader/__init__.py
+++ /dev/null
@@ -1,5 +0,0 @@
-from os import path
-from nd2reader.reader import ND2Reader
-from nd2reader.legacy import Nd2
-
-__version__ = '3.2.3'
diff --git a/nd2reader2/__init__.py b/nd2reader2/__init__.py
new file mode 100644
index 0000000..c712cb9
--- /dev/null
+++ b/nd2reader2/__init__.py
@@ -0,0 +1,5 @@
+from os import path
+from nd2reader2.reader import ND2Reader
+from nd2reader2.legacy import Nd2
+
+__version__ = '3.2.3'
diff --git a/nd2reader/artificial.py b/nd2reader2/artificial.py
similarity index 99%
rename from nd2reader/artificial.py
rename to nd2reader2/artificial.py
index 861c613..9f8aa04 100644
--- a/nd2reader/artificial.py
+++ b/nd2reader2/artificial.py
@@ -3,7 +3,7 @@
 import six
 import numpy as np
 import struct
-from nd2reader.common import check_or_make_dir
+from nd2reader2.common import check_or_make_dir
 from os import path
 
 global_labels = ['image_attributes', 'image_text_info', 'image_metadata',
diff --git a/nd2reader/common.py b/nd2reader2/common.py
similarity index 90%
rename from nd2reader/common.py
rename to nd2reader2/common.py
index df5ddcf..927e8d3 100644
--- a/nd2reader/common.py
+++ b/nd2reader2/common.py
@@ -1,10 +1,11 @@
 import os
 import struct
 import array
+import functools
 from datetime import datetime
 import six
 import re
-from nd2reader.exceptions import InvalidVersionError
+from nd2reader2.exceptions import InvalidVersionError
 
 
 def get_version(fh):
@@ -144,7 +145,7 @@ def _parse_double(data):
     return struct.unpack("d", data.read(8))[0]
 
 
-def _parse_string(data):
+def _parse_string(data, utf8encode=True):
     """
 
         Args:
@@ -163,9 +164,12 @@ def _parse_string(data):
         value += next_data
 
     try:
-        decoded = value.decode("utf16")[:-1].encode("utf8")
+        decoded = value.decode("utf16")[:-1]
     except UnicodeDecodeError:
-        decoded = value.decode('utf8').encode("utf8")
+        decoded = value.decode('utf8')
+
+    if utf8encode:
+        decoded = decoded.encode("utf8")
 
     return decoded
 
@@ -209,7 +213,7 @@ def parse_date(text_info):
     return None
 
 
-def _parse_metadata_item(data, cursor_position):
+def _parse_metadata_item(data, cursor_position, utf8encode=True):
     """Reads hierarchical data, analogous to a Python dict.
 
     Args:
@@ -223,7 +227,7 @@ def _parse_metadata_item(data, cursor_position):
     new_count, length = struct.unpack("<IQ", data.read(12))
     length -= data.tell() - cursor_position
     next_data_length = data.read(length)
-    value = read_metadata(next_data_length, new_count)
+    value = read_metadata(next_data_length, new_count, utf8encode=utf8encode)
 
     # Skip some offsets
     data.read(new_count * 8)
@@ -231,7 +235,7 @@ def _parse_metadata_item(data, cursor_position):
     return value
 
 
-def _get_value(data, data_type, cursor_position):
+def _get_value(data, data_type, cursor_position, utf8encode=True):
     """ND2s use various codes to indicate different data types, which we translate here.
 
     Args:
@@ -249,9 +253,9 @@ def _get_value(data, data_type, cursor_position):
               3: _parse_unsigned_int,
               5: _parse_unsigned_long,
               6: _parse_double,
-              8: _parse_string,
+              8: functools.partial(_parse_string, utf8encode=utf8encode),
               9: _parse_char_array,
-              11: _parse_metadata_item}
+              11: functools.partial(_parse_metadata_item, utf8encode=utf8encode)}
     try:
         value = parser[data_type](data) if data_type < 11 else parser[data_type](data, cursor_position)
     except (KeyError, struct.error):
@@ -260,7 +264,7 @@ def _get_value(data, data_type, cursor_position):
     return value
 
 
-def read_metadata(data, count):
+def read_metadata(data, count, utf8encode=True):
     """
     Iterates over each element of some section of the metadata and parses it.
 
@@ -287,8 +291,11 @@ def read_metadata(data, count):
             break
 
         data_type, name_length = struct.unpack('BB', header)
-        name = data.read(name_length * 2).decode("utf16")[:-1].encode("utf8")
-        value = _get_value(data, data_type, cursor_position)
+        name = data.read(name_length * 2).decode("utf16")[:-1]
+        value = _get_value(data, data_type, cursor_position, utf8encode=utf8encode)
+
+        if utf8encode:
+            name = name.encode("utf8")
 
         metadata = _add_to_metadata(metadata, name, value)
 
diff --git a/nd2reader/common_raw_metadata.py b/nd2reader2/common_raw_metadata.py
similarity index 98%
rename from nd2reader/common_raw_metadata.py
rename to nd2reader2/common_raw_metadata.py
index 422f521..b0853ab 100644
--- a/nd2reader/common_raw_metadata.py
+++ b/nd2reader2/common_raw_metadata.py
@@ -1,7 +1,7 @@
 import six
 import warnings
 
-from nd2reader.common import get_from_dict_if_exists
+from nd2reader2.common import get_from_dict_if_exists
 
 
 def parse_if_not_none(to_check, callback):
diff --git a/nd2reader/exceptions.py b/nd2reader2/exceptions.py
similarity index 100%
rename from nd2reader/exceptions.py
rename to nd2reader2/exceptions.py
diff --git a/nd2reader/label_map.py b/nd2reader2/label_map.py
similarity index 100%
rename from nd2reader/label_map.py
rename to nd2reader2/label_map.py
diff --git a/nd2reader/legacy.py b/nd2reader2/legacy.py
similarity index 99%
rename from nd2reader/legacy.py
rename to nd2reader2/legacy.py
index 9b010b8..8def57a 100644
--- a/nd2reader/legacy.py
+++ b/nd2reader2/legacy.py
@@ -4,7 +4,7 @@ Legacy class for backwards compatibility
 
 import warnings
 
-from nd2reader import ND2Reader
+from nd2reader2 import ND2Reader
 
 
 class Nd2(object):
diff --git a/nd2reader/parser.py b/nd2reader2/parser.py
similarity index 98%
rename from nd2reader/parser.py
rename to nd2reader2/parser.py
index bebbcaa..b702683 100644
--- a/nd2reader/parser.py
+++ b/nd2reader2/parser.py
@@ -7,10 +7,10 @@ import warnings
 from pims.base_frames import Frame
 import numpy as np
 
-from nd2reader.common import get_version, read_chunk
-from nd2reader.label_map import LabelMap
-from nd2reader.raw_metadata import RawMetadata
-from nd2reader import stitched
+from nd2reader2.common import get_version, read_chunk
+from nd2reader2.label_map import LabelMap
+from nd2reader2.raw_metadata import RawMetadata
+from nd2reader2 import stitched
 
 
 class Parser(object):
diff --git a/nd2reader/raw_metadata.py b/nd2reader2/raw_metadata.py
similarity index 98%
rename from nd2reader/raw_metadata.py
rename to nd2reader2/raw_metadata.py
index 3c25d57..3d62416 100644
--- a/nd2reader/raw_metadata.py
+++ b/nd2reader2/raw_metadata.py
@@ -4,8 +4,8 @@ import six
 import numpy as np
 import warnings
 
-from nd2reader.common import read_chunk, read_array, read_metadata, parse_date, get_from_dict_if_exists
-from nd2reader.common_raw_metadata import parse_dimension_text_line, parse_if_not_none, parse_roi_shape, parse_roi_type, get_loops_from_data, determine_sampling_interval
+from nd2reader2.common import read_chunk, read_array, read_metadata, parse_date, get_from_dict_if_exists
+from nd2reader2.common_raw_metadata import parse_dimension_text_line, parse_if_not_none, parse_roi_shape, parse_roi_type, get_loops_from_data, determine_sampling_interval
 
 
 class RawMetadata(object):
diff --git a/nd2reader/reader.py b/nd2reader2/reader.py
similarity index 98%
rename from nd2reader/reader.py
rename to nd2reader2/reader.py
index 295bded..1d7c8a8 100644
--- a/nd2reader/reader.py
+++ b/nd2reader2/reader.py
@@ -1,8 +1,8 @@
 from pims import Frame
 from pims.base_frames import FramesSequenceND
 
-from nd2reader.exceptions import EmptyFileError, InvalidFileType
-from nd2reader.parser import Parser
+from nd2reader2.exceptions import EmptyFileError, InvalidFileType
+from nd2reader2.parser import Parser
 import numpy as np
 
 
diff --git a/nd2reader/stitched.py b/nd2reader2/stitched.py
similarity index 100%
rename from nd2reader/stitched.py
rename to nd2reader2/stitched.py
diff --git a/setup.py b/setup.py
index bf52e5b..908d364 100644
--- a/setup.py
+++ b/setup.py
@@ -3,20 +3,20 @@ from setuptools import setup
 
 if __name__ == '__main__':
     setup(
-        name='nd2reader',
-        packages=['nd2reader'],
+        name='nd2reader2',
+        packages=['nd2reader2'],
         install_requires=[
             'numpy>=1.6.2',
             'six>=1.4',
             'xmltodict>=0.9.2',
             'PIMS>=0.5.0'
         ],
-        version="3.2.3-zolfa-dev0",
+        version="0.0.1",
         description='A tool for reading ND2 files produced by NIS Elements',
-        author='Ruben Verweij',
-        author_email='ruben@lighthacking.nl',
-        url='https://github.com/rbnvrw/nd2reader',
-        download_url='https://github.com/rbnvrw/nd2reader/tarball/%s' % "3.2.3-zolfa-dev0",
+        author='Lorenzo Zolfanelli',
+        author_email='dev@zolfa.nl',
+        url='https://projects.lilik.it/zolfa/nd2reader2',
+        download_url='https://github.com/rbnvrw/nd2reader2/tarball/%s' % "0.0.1",
         keywords=['nd2', 'nikon', 'microscopy', 'NIS Elements'],
         classifiers=['Development Status :: 5 - Production/Stable',
                      'Intended Audience :: Science/Research',
diff --git a/test.py b/test.py
index e5a6d6c..46e56b1 100644
--- a/test.py
+++ b/test.py
@@ -3,4 +3,4 @@ from os import path
 
 file_path = path.abspath(__file__)
 tests_path = path.join(path.abspath(path.dirname(file_path)), "tests")
-nose.main(argv=[path.abspath(__file__), "--with-coverage", "--cover-erase", "--cover-package=nd2reader", tests_path])
+nose.main(argv=[path.abspath(__file__), "--with-coverage", "--cover-erase", "--cover-package=nd2reader2", tests_path])
diff --git a/tests/test_artificial.py b/tests/test_artificial.py
index e9d2b29..247dcbe 100644
--- a/tests/test_artificial.py
+++ b/tests/test_artificial.py
@@ -3,10 +3,10 @@ from os import path
 import six
 import struct
 
-from nd2reader.artificial import ArtificialND2
-from nd2reader.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
+from nd2reader2.artificial import ArtificialND2
+from nd2reader2.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
     _parse_unsigned_int, _parse_unsigned_long, _parse_double, check_or_make_dir
-from nd2reader.exceptions import InvalidVersionError
+from nd2reader2.exceptions import InvalidVersionError
 
 
 class TestArtificial(unittest.TestCase):
diff --git a/tests/test_common.py b/tests/test_common.py
index 8e13aaa..c21eb7c 100644
--- a/tests/test_common.py
+++ b/tests/test_common.py
@@ -5,11 +5,11 @@ import array
 import six
 import struct
 
-from nd2reader.artificial import ArtificialND2
-from nd2reader.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
+from nd2reader2.artificial import ArtificialND2
+from nd2reader2.common import get_version, parse_version, parse_date, _add_to_metadata, _parse_unsigned_char, \
     _parse_unsigned_int, _parse_unsigned_long, _parse_double, check_or_make_dir, _parse_string, _parse_char_array, \
     get_from_dict_if_exists, read_chunk
-from nd2reader.exceptions import InvalidVersionError
+from nd2reader2.exceptions import InvalidVersionError
 
 
 class TestCommon(unittest.TestCase):
diff --git a/tests/test_label_map.py b/tests/test_label_map.py
index 1f58fd6..c1a9c12 100644
--- a/tests/test_label_map.py
+++ b/tests/test_label_map.py
@@ -1,6 +1,6 @@
 import unittest
-from nd2reader.label_map import LabelMap
-from nd2reader.artificial import ArtificialND2
+from nd2reader2.label_map import LabelMap
+from nd2reader2.artificial import ArtificialND2
 
 
 class TestLabelMap(unittest.TestCase):
diff --git a/tests/test_legacy.py b/tests/test_legacy.py
index 4c938cd..b363f52 100644
--- a/tests/test_legacy.py
+++ b/tests/test_legacy.py
@@ -1,9 +1,9 @@
 import unittest
 import warnings
 
-from nd2reader.legacy import Nd2
-from nd2reader.reader import ND2Reader
-from nd2reader.artificial import ArtificialND2
+from nd2reader2.legacy import Nd2
+from nd2reader2.reader import ND2Reader
+from nd2reader2.artificial import ArtificialND2
 
 
 class TestLegacy(unittest.TestCase):
diff --git a/tests/test_parser.py b/tests/test_parser.py
index c0b4ddf..ee61367 100644
--- a/tests/test_parser.py
+++ b/tests/test_parser.py
@@ -1,8 +1,8 @@
 import unittest
 from os import path
-from nd2reader.artificial import ArtificialND2
-from nd2reader.common import check_or_make_dir
-from nd2reader.parser import Parser
+from nd2reader2.artificial import ArtificialND2
+from nd2reader2.common import check_or_make_dir
+from nd2reader2.parser import Parser
 import urllib.request
 
 
diff --git a/tests/test_raw_metadata.py b/tests/test_raw_metadata.py
index c21e0fe..a364952 100644
--- a/tests/test_raw_metadata.py
+++ b/tests/test_raw_metadata.py
@@ -1,10 +1,10 @@
 import unittest
 import six
 
-from nd2reader.artificial import ArtificialND2
-from nd2reader.label_map import LabelMap
-from nd2reader.raw_metadata import RawMetadata
-from nd2reader.common_raw_metadata import parse_roi_shape, parse_roi_type, parse_dimension_text_line
+from nd2reader2.artificial import ArtificialND2
+from nd2reader2.label_map import LabelMap
+from nd2reader2.raw_metadata import RawMetadata
+from nd2reader2.common_raw_metadata import parse_roi_shape, parse_roi_type, parse_dimension_text_line
 
 
 class TestRawMetadata(unittest.TestCase):
diff --git a/tests/test_reader.py b/tests/test_reader.py
index c28399d..2a4ce76 100644
--- a/tests/test_reader.py
+++ b/tests/test_reader.py
@@ -3,10 +3,10 @@ import numpy as np
 import struct
 
 from pims import Frame
-from nd2reader.artificial import ArtificialND2
-from nd2reader.exceptions import EmptyFileError, InvalidFileType
-from nd2reader.reader import ND2Reader
-from nd2reader.parser import Parser
+from nd2reader2.artificial import ArtificialND2
+from nd2reader2.exceptions import EmptyFileError, InvalidFileType
+from nd2reader2.reader import ND2Reader
+from nd2reader2.parser import Parser
 
 
 class TestReader(unittest.TestCase):
diff --git a/tests/test_version.py b/tests/test_version.py
index fedfeeb..16de58e 100644
--- a/tests/test_version.py
+++ b/tests/test_version.py
@@ -1,5 +1,5 @@
 import unittest
-from nd2reader import __version__ as VERSION
+from nd2reader2 import __version__ as VERSION
 
 
 class TestVersion(unittest.TestCase):