Add distance z to layout (#147)

* switch to openjdk8 and force maven to use it for travis tests

* Added distanceZ attribute to layout component of tile spec to capture differing depth of FIBSEM tiles.

* add IntelliJ (PyCharm) editor files to .gitignore

* Bump version: 2.1.1 → 2.2.0

* Bump version: 2.2.0 → 2.3.0

Author: trautmane

.bumpversion.cfg

@@ -1,7 +1,6 @@
 [bumpversion]
-current_version = 2.1.1
+current_version = 2.3.0
 commit = True
 tag = True
 
 [bumpversion:file:renderapi/__init__.py]
-

.gitignore

@@ -13,4 +13,6 @@ htmlcov/
 .cache
 .tox
 .pytest_cache
-.vscode
+.vscode
+.idea/
+*.iml

.travis.yml

@@ -17,14 +17,16 @@ addons:
         - libopenblas-base
         - libopenblas-dev
         - gfortran
-        - oracle-java9-set-default
+        - openjdk-8-jdk
         - maven
 install:
   - pip install codecov
   - pip install -r requirements.txt
   - pip install -r test_requirements.txt
 before_install:
   - git clone --depth 1 https://github.com/saalfeldlab/render.git render -b master
+  - export JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/jre"
+  - mvn -version
   - mvn package -pl render-ws-java-client -am -DskipTests -f render/pom.xml
   - export RENDER_CLIENT_JAR=`readlink -m $TRAVIS_BUILD_DIR/render/render-ws-java-client/target/render-ws-java-client-*-standalone.jar`
   - export RENDER_WS_JAVA_CLIENT_EXAMPLE_DATA=`readlink -m $TRAVIS_BUILD_DIR/render/render-ws-java-client/src/main/resources`

renderapi/__init__.py

@@ -13,7 +13,7 @@
 from .render import connect
 from .render import Render
 
-__version__ = "2.1.1"
+__version__ = "2.3.0"
 __all__ = ['render', 'client', 'tilespec', 'errors',
            'stack', 'image', 'pointmatch', 'coordinate',
            'connect', 'transform', 'resolvedtiles', 'Render']

renderapi/layout.py

@@ -21,12 +21,14 @@ class Layout:
         angle of camera when this was taken
     pixelsize : float
         effective size of pixels (in units of choice)
+    distanceZ : float
+        distance (in units of choice) from prior layer
 
     """
     def __init__(self, sectionId=None, scopeId=None, cameraId=None,
                  imageRow=None, imageCol=None, stageX=None, stageY=None,
                  rotation=None, pixelsize=None,
-                 force_pixelsize=True, **kwargs):
+                 force_pixelsize=True, distanceZ=None, **kwargs):
         """Initialize Layout
 
         Parameters
@@ -51,6 +53,8 @@ def __init__(self, sectionId=None, scopeId=None, cameraId=None,
             effective size of pixels (in units of choice)
         force_pixelsize : bool
             whether to default pixelsize to 0.1
+        distanceZ : float
+            distance (in units of choice) from prior layer
 
         """
         self.sectionId = sectionId
@@ -64,6 +68,7 @@ def __init__(self, sectionId=None, scopeId=None, cameraId=None,
         if force_pixelsize:
             pixelsize = 0.100 if pixelsize is None else pixelsize
         self.pixelsize = pixelsize
+        self.distanceZ = distanceZ
 
     def to_dict(self):
         """return a dictionary representation of this object
@@ -83,6 +88,7 @@ def to_dict(self):
         d['stageY'] = self.stageY
         d['rotation'] = self.rotation
         d['pixelsize'] = self.pixelsize
+        d['distanceZ'] = self.distanceZ
         d = {k: v for k, v in d.items() if v is not None}
         return d
 
@@ -104,3 +110,4 @@ def from_dict(self, d):
             self.stageY = d.get('stageY')
             self.rotation = d.get('rotation')
             self.pixelsize = d.get('pixelsize')
+            self.distanceZ = d.get('distanceZ')