Merge pull request #17 from Steven-N-Hart/renaming_modules

Renaming modules

Dockerfile

@@ -11,7 +11,7 @@ RUN cd dicom_wsi && pip3 install -r requirements.txt && cd /
 ENV PYTHONPATH=$PYTHONPATH:/dicom_wsi/dicom_wsi/mods/
 #
 ## Add other tools
-##Google
+## Google
 #RUN wget https://github.com/GoogleCloudPlatform/wsi-to-dicom-converter/releases/download/v1.0.3/wsi2dcm_1.0.3.deb
 #RUN apt install ./wsi2dcm_1.0.3.deb
 #

__init__.py

@@ -0,0 +1,20 @@
+__author__ = """Steven N. Hart"""
+__email__ = '[email protected]'
+__version__ = '1.0.0'
+from .dicom_wsi import add_annotations
+from .dicom_wsi import base_attributes
+from .dicom_wsi import character_validations
+from .dicom_wsi import cli
+from .dicom_wsi import dicom_wsi
+from .dicom_wsi import extract_annotations
+from .dicom_wsi import extract_image_patches
+from .dicom_wsi import image_filter
+from .dicom_wsi import input_validation
+from .dicom_wsi import mapping
+from .dicom_wsi import parse_wsi
+from .dicom_wsi import pixel_data_conversion
+from .dicom_wsi import pixel_to_slide_conversions
+from .dicom_wsi import run
+from .dicom_wsi import sequence_attributes
+from .dicom_wsi import shared_functional_groups
+from .dicom_wsi import utils

dicom_wsi/__init__.py

@@ -2,4 +2,5 @@
 """Top-level package for dicom-wsi."""
 __author__ = """Steven N. Hart"""
 __email__ = '[email protected]'
-__version__ = '0.1.0'
+__version__ = '1.0.0'
+

dicom_wsi/mods/base_attributes.py → dicom_wsi/base_attributes.py

@@ -3,10 +3,9 @@
 import tempfile
 
 import pydicom
-from pydicom.dataset import Dataset, FileDataset
+from pydicom.dataset import FileMetaDataset, FileDataset
 
 # noinspection PyUnresolvedReferences,PyUnresolvedReferences,PyUnresolvedReferences
-# from mods.utils import add_data
 from .utils import add_data
 
 
@@ -40,7 +39,8 @@ def build_base(cfg, instance=1):
     suffix = '.' + str(instance) + '.dcm'
     filename_little_endian = tempfile.NamedTemporaryFile(suffix=suffix).name
 
-    file_meta = Dataset()
+    # file_meta = Dataset() # deprecated in pydicom 3.0
+    file_meta = FileMetaDataset()
 
     if compression_type == 'None':
         # noinspection PyPep8,PyUnresolvedReferences

dicom_wsi/cli.py

@@ -6,7 +6,7 @@
 import os
 import sys
 
-from mods import parse_wsi
+from . import parse_wsi
 from yaml import load, BaseLoader
 
 import dicom_wsi

dicom_wsi/dicom_wsi.py

@@ -1,8 +1,8 @@
 # -*- coding: utf-8 -*-
 import logging
 
-from mods.input_validation import validate_cfg
-from mods.run import run_instance
+from .input_validation import validate_cfg
+from .run import run_instance
 
 logger = logging.getLogger(__name__)
 import multiprocessing as mp

docs/gettingstarted.rst

@@ -76,8 +76,9 @@ To use dicom-wsi in a project:
 .. code-block:: python
 
     from yaml import load, BaseLoader
-    from dicom_wsi import create_dicom
-    from parse_wsi import get_wsi
+    import dicom_wsi
+    dwsi = dicom_wsi.dicom_wsi
+    get_wsi = dicom_wsi.parse_wsi.get_wsi
 
     # Define your YAML file
     my_yaml = '/path/to/yaml'
@@ -86,7 +87,7 @@ To use dicom-wsi in a project:
     # Read the WSI, updating the config with information contained in the slide
     cfg, wsi = get_wsi(cfg)
     # Create DICOM files
-    create_dicom(cfg)
+    dwsi.create_dicom(cfg)
 
 
 Sample RUN

docs/tldr.rst

@@ -2,11 +2,19 @@
 TL;DR
 =====
 
-To use dicom-wsi in a project:
+To use dicom-wsi in a project, you can run in one of two ways. You can run the command line program,
 
 .. code-block:: console
 
-    python cli.py cli.py -w <WSI File path> -o <OutputDirectory> -p <output file prefix> -y yaml/base.yaml
+    python cli.py -w <WSI File path> -o <OutputDirectory> -p <output file prefix> -y yaml/base.yaml
 
+Or you can run it directly from python
+
+.. code-block:: python
+
+    import dicom_wsi
+    dicom_wsi.dicom_wsi.create_dicom(cfg, pools=n_pools)
+
+The `cfg` is the dictionary of required entities, and n_pools defines the number of threads to use.
 
 That's it!

setup.py

@@ -46,7 +46,7 @@
     include_package_data=True,
     keywords='dicom_wsi',
     name='dicom_wsi',
-    packages=find_packages(include=['dicom_wsi', 'dicom_wsi.*']),
+    packages=find_packages(),
     setup_requires=setup_requirements,
     test_suite='tests',
     tests_require=test_requirements,

tests/test_base_attributes.py

@@ -7,8 +7,8 @@
 
 from yaml import load, BaseLoader
 
-from ..dicom_wsi.mods.base_attributes import build_base
-from ..dicom_wsi.mods.parse_wsi import *
+from ..dicom_wsi.base_attributes import build_base
+from ..dicom_wsi.parse_wsi import get_wsi
 
 
 def test_get_wsi():

tests/test_character_validations.py

@@ -2,13 +2,9 @@
 # -*- coding: utf-8 -*-
 
 """Tests for `dicom_wsi` package."""
-import os
-import sys
-
-sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '..')))
 import pytest
+from ..dicom_wsi import character_validations as cv
 
-from ..dicom_wsi.mods import character_validations as cv
 
 def test_cs():
     cv.cs_validator('patient', 'Roberto')

tests/test_sequence_attributes.py

@@ -7,9 +7,9 @@
 
 from yaml import load, BaseLoader
 
-from ..dicom_wsi.mods.base_attributes import build_base
-from ..dicom_wsi.mods.parse_wsi import *
-from ..dicom_wsi.mods.sequence_attributes import build_sequences
+from ..dicom_wsi.base_attributes import build_base
+from ..dicom_wsi.parse_wsi import get_wsi
+from ..dicom_wsi.sequence_attributes import build_sequences
 
 
 def test_get_wsi():

tests/test_shared_functional_groups.py

@@ -7,10 +7,10 @@
 
 from yaml import load, BaseLoader
 
-from ..dicom_wsi.mods.base_attributes import build_base
-from ..dicom_wsi.mods.parse_wsi import *
-from ..dicom_wsi.mods.sequence_attributes import build_sequences
-from ..dicom_wsi.mods.shared_functional_groups import build_functional_groups
+from ..dicom_wsi.base_attributes import build_base
+from ..dicom_wsi.parse_wsi import get_wsi
+from ..dicom_wsi.sequence_attributes import build_sequences
+from ..dicom_wsi.shared_functional_groups import build_functional_groups
 
 
 def test_get_wsi():