Merge pull request #113 from dvm-shlee/main

remove shleeh dependency v0.3.8

.gitignore

@@ -11,4 +11,5 @@ build
 test
 test/*
 *.egg-info
-*.egg-info/*
+*.egg-info/*
+.DS_Store

brkraw/__init__.py

@@ -1,6 +1,6 @@
 from .lib import *
 
-__version__ = '0.3.8-rc1'
+__version__ = '0.3.8'
 __all__ = ['BrukerLoader', '__version__']
 
 

brkraw/lib/backup.py

@@ -1,8 +1,6 @@
-from shleeh import *
-from shleeh.utils import *
-from shleeh.errors import *
+from .errors import *
 from .loader import BrukerLoader
-from .utils import get_dirsize, get_filesize, yes_or_no
+from .utils import get_dirsize, get_filesize, yes_or_no, TimeCounter
 import os
 import sys
 import tqdm

brkraw/lib/errors.py

@@ -0,0 +1,125 @@
+import os
+
+
+def print_internal_error(io_handler=None):
+    import traceback
+    import sys
+    if io_handler is None:
+        io_handler = sys.stderr
+    traceback.print_exception(*sys.exc_info(),
+                              file=io_handler)
+
+
+class Error(Exception):
+    """ Base class for other custom exceptions """
+    message = None
+
+
+class FileNotValidError(Error):
+    """ Raised when the file is not valid format """
+
+    def __init__(self, file_name=None, data_type=None):
+        self.file_name = None
+        self.data_type = None
+
+        if file_name is not None:
+            self.file_name = os.path.basename(file_name)
+            if os.path.isdir(file_name):
+                object_type = 'directory'
+            else:
+                object_type = 'file'
+            if data_type is not None:
+                self.data_type = data_type
+                self.message = "The {} '{}' is not valid {}".format(object_type,
+                                                                    self.file_name,
+                                                                    self.data_type)
+            else:
+                self.message = "The {} '{}' is not valid".format(object_type,
+                                                                 self.file_name)
+        else:
+            self.message = "The file is not valid"
+
+
+class ArchiveFailedError(Error):
+    """ Raised when the archive process is failed [designed for brkraw module] """
+    file_name = None
+
+    def __init__(self, file_name=None):
+        if file_name is not None:
+            self.file_name = os.path.basename(file_name)
+            self.message = "The data '{}' is not archived".format(
+                self.file_name)
+        else:
+            self.message = "Archive failed to execute"
+
+
+class RemoveFailedError(Error):
+    """ Raise when the os.remove process is failed """
+    file_name = None
+
+    def __init__(self, file_name=None):
+        if file_name is not None:
+            self.file_name = os.path.basename(file_name)
+            self.message = "The file '{}' is not removed".format(
+                self.file_name)
+        else:
+            self.message = "Remove failed to execute"
+
+
+class RenameFailedError(Error):
+    """ Raised when the os.rename process is failed (OSError)"""
+    file1_name = None
+    file2_name = None
+
+    def __init__(self, file1_name=None, file2_name=None):
+        if file1_name is not None:
+            self.file1_name = os.path.basename(file1_name)
+        if file2_name is not None:
+            self.file2_name = os.path.basename(file2_name)
+        if (self.file1_name is not None) and (self.file2_name is not None):
+            self.message = "Rename failed to execute from:'{}' to:'{}'".format(self.file1_name,
+                                                                               self.file2_name)
+        else:
+            self.message = "Rename failed to execute"
+
+
+class UnexpectedError(Error):
+    """ Raised when unexpected error occurred """
+
+    def __init__(self, message=None):
+        print_internal_error()
+        if message is None:
+            self.message = "Unexpected error"
+        else:
+            self.message = message
+
+
+class ValueConflictInField(Error):
+    """ Raised when input value was conflicted with other """
+
+    def __init__(self, message=None):
+        if message is None:
+            self.message = "The value is conflicted"
+        else:
+            self.message = message
+
+
+class InvalidValueInField(Error):
+    """ Raise when the invalid value is detected in field """
+
+    def __init__(self, message=None):
+        if message is None:
+            self.message = "Invalid value is detected"
+        else:
+            self.message = message
+
+
+class InvalidApproach(Error):
+    """ Raise when the user try invalid approach """
+
+    def __init__(self, message=None):
+        print_internal_error()
+        if message is None:
+            self.message = "Invalid approach!"
+        else:
+            self.message = message

brkraw/lib/loader.py

@@ -1,6 +1,4 @@
-from shleeh import *
-from shleeh.errors import *
-
+from .errors import *
 from .orient import build_affine_from_orient_info, reversed_pose_correction, get_origin
 from .pvobj import PvDatasetDir, PvDatasetZip
 from .utils import *
@@ -13,6 +11,13 @@
 import re
 import warnings
 np.set_printoptions(formatter={'float_kind':'{:f}'.format})
+import enum
+
+
+@enum.unique
+class DataType(enum.Enum):
+    PVDATASET = 1
+    NIFTI1 = 2
 
 
 def load(path):

brkraw/lib/utils.py

@@ -1,12 +1,25 @@
-from shleeh.errors import UnexpectedError
-
+from .errors import UnexpectedError
 from .reference import *
 import re
 import os
 import numpy as np
 from collections import OrderedDict
 from functools import partial, reduce
 from copy import copy as cp
+import time
+
+
+class TimeCounter:
+    _start = None
+
+    def __init__(self):
+        self.reset()
+
+    def reset(self):
+        self._start = time.time()
+
+    def time(self):
+        return time.time() - self._start
 
 
 def load_param(stringlist):

brkraw/scripts/brkraw.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
 from operator import index
-from shleeh import *
-from shleeh.errors import *
-
+from ..lib.errors import *
 from .. import BrukerLoader, __version__
 from ..lib.utils import set_rescale, save_meta_files, mkdir
 import argparse

setup.py

@@ -25,8 +25,7 @@
       url=__url__,
       license='GNLv3',
       packages=find_packages(),
-      install_requires=['shleeh>=0.1.0',
-                        'nibabel>=3.0.2',
+      install_requires=['nibabel>=3.0.2',
                         'numpy>=1.18.0',
                         'pandas>=1.0.0',
                         'pillow>=7.1.1',
@@ -47,7 +46,6 @@
             'Intended Audience :: Science/Research',
             'Topic :: Scientific/Engineering :: Medical Science Apps.',
             'Natural Language :: English',
-            'Programming Language :: Python :: >3.5'
       ],
       keywords = 'bruker data_handler converter administrator_tool'
      )