Microjson light doc

.gitignore

@@ -2,3 +2,5 @@
 tests/__pycache__/
 src/microjson/__pycache__/
 poetry.lock
+tmp*
+dist/*

README.md

@@ -2,6 +2,9 @@
 
 MicroJSON is a JSON-based format inspired by [GeoJSON](https://geojson.org), designed to encode a variety of data structures related to microscopy images. It can handle representations of reference points, regions of interest, and other annotations, making it an ideal solution for conveying complex microscopy data in a straightforward, easy-to-use format.
 
+For more extensive documentation, please refer to the [online documentation](https://polusai.github.io/microjson/).
+
+
 ## Features
 
 MicroJSON offers a range of features designed to meet the needs of microscopy data representation:
@@ -19,6 +22,16 @@ There are two additional functionalities added which supports binary and label i
 
 - **MicrojsonBinaryModel:** Reconstruct binary images using polygon coordinates from json file.
 
+## Installation
+
+To install MicroJSON, you can use the following command:
+
+```pip install microjson```
+This will install the default version of MicroJSON with the basic functionalities and minimal dependencies. If you want to use the additional functionalities, such as provided by the ```utils``` module, you can install the package with the following command:
+
+```pip install microjson[all]```
+
+
 ## Usage
 
 MicroJSON can be used with any application or tool that can process JSON data. Due to its design, it is particularly suited to applications related to the analysis, visualization, and manipulation of microscopy images.

README_short.md

@@ -17,6 +17,15 @@ There are two additional functionalities added which supports binary images.
 **BinaryMicrojsonModel:** Converts objects in a binary image into polygon coordinates (rectangle, encoding) and save them in json file format using microjson package.
 **MicrojsonBinaryModel:** Reconstruct binary images using polygon coordinates from json file.
 
+## Installation
+
+To install MicroJSON, you can use the following command:
+
+```pip install microjson```
+This will install the default version of MicroJSON with the basic functionalities and minimal dependencies. If you want to use the additional functionalities, such as provided by the ```utils``` module, you can install the package with the following command:
+
+```pip install microjson[all]```
+
 ## Usage
 
 MicroJSON can be used with any application or tool that can process JSON data. Due to its design, it is particularly suited to applications related to the analysis, visualization, and manipulation of microscopy images.
@@ -31,10 +40,7 @@ We welcome contributions to the development and enhancement of MicroJSON. Whethe
 
 ## License
 
-MicroJSON is licensed under MIT License, (c) 2023 Polus AI & Nextonic Solutions LLC.
-
-## Authors
-Bengt Ljungquist [[email protected]]([email protected])
+MicroJSON is licensed under MIT License.
 
 
 ---

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "microjson"
-version = "0.1.11"
+version = "0.2.0"
 description = "MicroJSON is a library for validating, parsing, and manipulating MicroJSON data."
 readme = "README_short.md"
 authors = ["Bengt Ljungquist <[email protected]>"]
@@ -28,33 +28,43 @@ where = ["src"]
 [tool.poetry.dependencies]
 python = ">=3.9.15,<3.12"
 pydantic = "^2.3.0"
-scikit-image = "0.20.0"
 geojson-pydantic = "^1.0.2"
+jsonschema = "^4.0.0"
+
+
+[tool.poetry.dependencies.scikit-image]
+version = "^0.20.0"
+optional = true
 
 
 [tool.poetry.dependencies.bfio]     
-version = "2.3.6"
-extras = ["all"]   
+version = "0.2.0" 
 optional = true
 
 [tool.poetry.dependencies.scipy]     
-version = ">=1.8,<1.9.2"
+version = "^1.9.1"
 optional = true
 
 [tool.poetry.dependencies.filepattern] 
 version = "^2.0.1"
 optional = true
 
-[tool.poetry.dependencies.vaex]      
-version = "^4.17.0"
+[tool.poetry.dependencies.vaex-core]      
+version = "^4.8.0"
+optional = true
+
+[tool.poetry.dependencies.matplotlib]
+version = "^3.5.1"
 optional = true
 
 [tool.poetry.extras]
 all = [
     "bfio", 
     "scipy", 
     "filepattern", 
-    "vaex"
+    "vaex-core",
+    "scikit-image",
+    "matplotlib",
 ]
 
 [tool.poetry.dev-dependencies]
@@ -74,7 +84,7 @@ mkdocstrings = "^0.23.0"
 testpaths = ["tests/"]
 
 [tool.bumpver]
-current_version = "0.1.11"
+current_version = "0.2.0"
 version_pattern = "MAJOR.MINOR.PATCH"
 commit_message  = "Bump version {old_version} -> {new_version}"
 commit          = true

src/microjson/__init__.py

@@ -1,4 +1,4 @@
 from .model import MicroJSON, GeoJSON
 
 
-__version__ = "0.1.11"
+__version__ = "0.2.0"

src/microjson/model.py

@@ -68,6 +68,14 @@ class Unit(Enum):
     PIXEL = "pixel"
     RADIAN = "radian"
     DEGREE = "degree"
+    MILLISECOND = "millisecond"
+    SECOND = "second"
+    MINUTE = "minute"
+    HOUR = "hour"
+    DAY = "day"
+    WEEK = "week"
+    MONTH = "month"
+    YEAR = "year"
 
 
 class AxisType(Enum):

src/microjson/utils.py

@@ -30,17 +30,6 @@
 import pydantic
 import matplotlib.pyplot as plt
 
-#define conditional imports
-try:
-    from bfio import BioReader
-    import filepattern as fp
-    from scipy import ndimage
-    import vaex
-except ImportError as e:
-    print("""Packages bfio, filepattern, scipy, vaex not installed
-          please install using pip install microjson[all]""")
-    raise e
-
 
 #define conditional imports
 try:

tests/test_utils.py

@@ -6,13 +6,14 @@
 import tempfile
 from pathlib import Path
 from typing import Union
-import numpy as np
 import pytest
-import skimage as sk
+
 HAS_BFIO = False
 try:
     import bfio
     HAS_BFIO = True
+    import numpy as np
+    import skimage as sk
 except ImportError:
     pass