Add 'get_plane' functionality (Arcadia-Science#23)

ilorevilo · Apr 20, 2021 · af0bfa6 · af0bfa6
1 parent fa42ab7
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diff --git a/.sync-conflict-20210420-161022-LU5YQDC.DS_Store b/.sync-conflict-20210420-161022-LU5YQDC.DS_Store
diff --git a/.syncthing..DS_Store.tmp b/.syncthing..DS_Store.tmp
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 [![Documentation Status](https://readthedocs.org/projects/readlif/badge/?version=latest)](https://readlif.readthedocs.io/en/latest/?badge=latest)
 [![CI-Tests](https://github.com/nimne/readlif/workflows/CI-Tests/badge.svg)](https://github.com/nimne/readlif/actions?query=workflow%3ACI-Tests)
 
-readlif README file
+readlif README file - DEVELOPMENT BRANCH
 ===
 The readlif package was developed to be a fast, python only, reader for Leica Lif files. This is tested in Python 3.6 through 3.9.
 
@@ -31,6 +31,11 @@ this is not tested. If you have an example file, open an issue!
 There is not support for FlipX, FlipY and SwapXY metadata. If you need this, 
 please open an issue!
 
+Truncated images are returned as blank images.
+
+There is currently no support for returning arbitrary planes from `get_plane`
+by specifying `display_dims`. This is in progress.
+
 12- and 16-bit images
 ===
 As of 0.3.0, `reaflif` will now support images with bit depth greater than 8.
@@ -87,8 +92,12 @@ This has only been tested on Lif files that were generated with Leica LAS X and
 
 Changelog
 ======
+#### 0.6.0
+- Added support for non-XY images with `get_plane()`. See docs for usage.
+    - Note: Reading arbitrary planes (i.e. an XZ plane of an XY image) is not yet supported. 
+
 #### 0.5.2
-- Bugfix: Fix error in mosaic parsing. `PosX` metadata was incorrectly read from `Posy`
+- Bugfix: Fix error in mosaic parsing. `PosX` metadata was incorrectly read from `PosY`
 
 #### 0.5.1
 - Bugfix: switch from `io.BufferedIOBase` to `io.IOBase`

diff --git a/docs/conf.py b/docs/conf.py
@@ -19,11 +19,11 @@
 # -- Project information -----------------------------------------------------
 
 project = "readlif"
-copyright = "2019, Nick Negretti"
+copyright = "2021, Nick Negretti"
 author = "Nick Negretti"
 
 # The full version, including alpha/beta/rc tags
-release = "0.5.1"
+release = "0.6.0"
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/source/readlif.reader.rst b/docs/source/readlif.reader.rst
@@ -2,6 +2,6 @@ readlif.reader module
 =====================
 
 .. automodule:: readlif.reader
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/readlif.rst b/docs/source/readlif.rst
@@ -5,6 +5,7 @@ Submodules
 ----------
 
 .. toctree::
+   :maxdepth: 4
 
    readlif.reader
    readlif.utilities
@@ -13,6 +14,6 @@ Module contents
 ---------------
 
 .. automodule:: readlif
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/readlif.utilities.rst b/docs/source/readlif.utilities.rst
@@ -2,6 +2,6 @@ readlif.utilities module
 ========================
 
 .. automodule:: readlif.utilities
-    :members:
-    :undoc-members:
-    :show-inheritance:
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/readlif/__init__.py b/readlif/__init__.py
@@ -1 +1 @@
-__version__ = "0.5.1"
+__version__ = "0.6.0"