Merge pull request #80 from jimrybarski/dev

Dev

.dockerignore

@@ -0,0 +1,11 @@
+.gitignore
+.git
+*.md
+*.txt
+Dockerfile
+Makefile
+setup.cfg
+env
+*.egg-info
+build
+dist

Dockerfile

@@ -15,6 +15,8 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     python3-dev \
     python-pip \
     python3-pip \
+    python-numpy \
+    python3-numpy \
     libfreetype6-dev \
     python3-matplotlib \
     libfreetype6-dev \
@@ -22,6 +24,9 @@ RUN apt-get update && apt-get install -y --no-install-recommends \
     libjpeg-dev \
     pkg-config \
     python3-skimage \
+    tk \
+    tk-dev \
+    python3-tk \
  && pip3 install -U cython \
     scikit-image \
  && rm -rf /var/lib/apt/lists/*

Makefile

@@ -1,13 +1,26 @@
-.PHONY: build py2shell py3shell test
+.PHONY: info build shell py2 py3 test
+
+info:
+	@echo ""
+	@echo "Available Make Commands"
+	@echo ""
+	@echo "build:	builds the image"
+	@echo "py2:	maps ~/Documents/nd2s to /var/nd2s and runs a Python 2.7 interpreter"
+	@echo "py3:	maps ~/Documents/nd2s to /var/nd2s and runs a Python 3.4 interpreter"
+	@echo "test:	runs all unit tests (in Python 3.4)"
+	@echo ""
 
 build:
 	docker build -t jimrybarski/nd2reader .
 
+shell:
+	xhost local:root; docker run --rm -v ~/Documents/nd2s:/var/nd2s -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -it jimrybarski/nd2reader bash
+
 py2:
-	docker run --rm -v ~/Documents/nd2s:/var/nd2s -it jimrybarski/nd2reader python2.7
+	xhost local:root; docker run --rm -v ~/Documents/nd2s:/var/nd2s -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -it jimrybarski/nd2reader python2.7
 
 py3:
-	docker run --rm -v ~/Documents/nd2s:/var/nd2s -it jimrybarski/nd2reader python3.4
+	xhost local:root; docker run --rm -v ~/Documents/nd2s:/var/nd2s -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=unix$(DISPLAY) -it jimrybarski/nd2reader python3.4
 
 test:	build
 	docker run --rm -it jimrybarski/nd2reader python3.4 /opt/nd2reader/tests.py

nd2reader/__init__.py

@@ -57,7 +57,8 @@ class Nd2(Nd2Parser):
                 fov = self._calculate_field_of_view(item)
                 channel = self._calculate_channel(item)
                 z_level = self._calculate_z_level(item)
-                timestamp, raw_image_data = self._get_raw_image_data(item, channel_offset)
+                image_group_number = int(item / len(self.channels))
+                timestamp, raw_image_data = self._get_raw_image_data(image_group_number, channel_offset)
                 image = Image(timestamp, raw_image_data, fov, channel, z_level, self.height, self.width)
             except (TypeError, ValueError):
                 return None

nd2reader/parser.py

@@ -234,8 +234,10 @@ class Nd2Parser(object):
         except AttributeError:
             return [0]
         except TypeError:
-            count = int(re.match(pattern, self._dimensions.decode("utf8")).group(1))
-            return list(range(count))
+            match = re.match(pattern, self._dimensions.decode("utf8"))
+            if not match:
+                return [0]
+            return list(range(int(match.group(1))))
         else:
             return list(range(count))