From 99c26b474f88be6580b241dfc98f0a97e3e67c38 Mon Sep 17 00:00:00 2001
From: Jim Rybarski <jim@rybarski.com>
Date: Sat, 16 May 2015 23:42:59 +0000
Subject: [PATCH] added makefile, simplified the Dockerfile

---
 Dockerfile                  | 22 +++++--------------
 Makefile                    |  7 ++++++
 nd2reader/model/__init__.py | 44 ++++++++++++++++++-------------------
 nd2reader/parser.py         |  8 +++----
 4 files changed, 39 insertions(+), 42 deletions(-)
 create mode 100644 Makefile

diff --git a/Dockerfile b/Dockerfile
index 95602c0..51e6ff0 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,24 +1,14 @@
 FROM ubuntu
 MAINTAINER Jim Rybarski <jim@rybarski.com>
 
+RUN mkdir -p /var/nds2
 RUN apt-get update && apt-get install -y \
-  gcc \
-  gfortran \
-  libblas-dev \
-  liblapack-dev \
-  libatlas-dev \
-  tk \
-  tk-dev \
-  libpng12-dev \  
-  python \
-  python-dev \
-  python-pip \
-  libfreetype6-dev \
-  python-skimage
- 
-RUN pip install numpy
-RUN pip install --upgrade scikit-image
+    python-numpy \
+    python-setuptools
 
 COPY . /opt/nd2reader
 WORKDIR /opt/nd2reader
 RUN python setup.py install
+WORKDIR /var/nd2s
+
+CMD /usr/bin/python2.7
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..30e5e42
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,7 @@
+.PHONY: build test shell
+
+build:
+	docker build -t jimrybarski/nd2reader .
+
+shell:
+	docker run --rm -v ~/Documents/nd2s:/var/nd2s -it jimrybarski/nd2reader
diff --git a/nd2reader/model/__init__.py b/nd2reader/model/__init__.py
index 4d59b4d..64bf398 100644
--- a/nd2reader/model/__init__.py
+++ b/nd2reader/model/__init__.py
@@ -4,27 +4,6 @@ import logging
 log = logging.getLogger(__name__)
 
 
-class ImageSet(object):
-    """
-    A group of images that share the same timestamp. NIS Elements doesn't store a unique timestamp for every
-    image, rather, it stores one for each set of images that share the same field of view and z-axis level.
-
-    """
-    def __init__(self):
-        self._images = []
-
-    def add(self, image):
-        """
-        :type image:    nd2reader.model.Image()
-
-        """
-        self._images.append(image)
-
-    def __iter__(self):
-        for image in self._images:
-            yield image
-
-
 class Image(object):
     def __init__(self, timestamp, raw_array, field_of_view, channel, z_level, height, width):
         self._timestamp = timestamp
@@ -68,4 +47,25 @@ class Image(object):
 
     @property
     def is_valid(self):
-        return np.any(self._raw_data)
\ No newline at end of file
+        return np.any(self._raw_data)
+
+
+class ImageSet(object):
+    """
+    A group of images that share the same timestamp. NIS Elements doesn't store a unique timestamp for every
+    image, rather, it stores one for each set of images that share the same field of view and z-axis level.
+
+    """
+    def __init__(self):
+        self._images = []
+
+    def add(self, image):
+        """
+        :type image:    nd2reader.model.Image()
+
+        """
+        self._images.append(image)
+
+    def __iter__(self):
+        for image in self._images:
+            yield image
\ No newline at end of file
diff --git a/nd2reader/parser.py b/nd2reader/parser.py
index 0aaa705..ee49d53 100644
--- a/nd2reader/parser.py
+++ b/nd2reader/parser.py
@@ -9,14 +9,14 @@ field_of_view = namedtuple('FOV', ['number', 'x', 'y', 'z', 'pfs_offset'])
 
 
 class Nd2Parser(object):
-    CHUNK_HEADER = 0xabeceda
-    CHUNK_MAP_START = "ND2 FILEMAP SIGNATURE NAME 0001!"
-    CHUNK_MAP_END = "ND2 CHUNK MAP SIGNATURE 0000001!"
-    
     """
     Reads .nd2 files, provides an interface to the metadata, and generates numpy arrays from the image data.
 
     """
+    CHUNK_HEADER = 0xabeceda
+    CHUNK_MAP_START = "ND2 FILEMAP SIGNATURE NAME 0001!"
+    CHUNK_MAP_END = "ND2 CHUNK MAP SIGNATURE 0000001!"
+    
     def __init__(self, filename):
         self._absolute_start = None
         self._filename = filename