Repository: incubator-systemml Updated Branches: refs/heads/master 240569420 -> a11374b89
[SYSTEMML-1185] Minor updates to the breast cancer project. Project: http://git-wip-us.apache.org/repos/asf/incubator-systemml/repo Commit: http://git-wip-us.apache.org/repos/asf/incubator-systemml/commit/a11374b8 Tree: http://git-wip-us.apache.org/repos/asf/incubator-systemml/tree/a11374b8 Diff: http://git-wip-us.apache.org/repos/asf/incubator-systemml/diff/a11374b8 Branch: refs/heads/master Commit: a11374b890052dd9041eebaabac7dfff3f7d37c7 Parents: 2405694 Author: Mike Dusenberry <mwdus...@us.ibm.com> Authored: Mon Feb 6 14:48:12 2017 -0800 Committer: Mike Dusenberry <mwdus...@us.ibm.com> Committed: Mon Feb 6 14:48:12 2017 -0800 ---------------------------------------------------------------------- projects/breast_cancer/Preprocessing.ipynb | 15 ++++++++------- projects/breast_cancer/README.md | 4 ++-- 2 files changed, 10 insertions(+), 9 deletions(-) ---------------------------------------------------------------------- http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/a11374b8/projects/breast_cancer/Preprocessing.ipynb ---------------------------------------------------------------------- diff --git a/projects/breast_cancer/Preprocessing.ipynb b/projects/breast_cancer/Preprocessing.ipynb index a54e862..ed647b9 100644 --- a/projects/breast_cancer/Preprocessing.ipynb +++ b/projects/breast_cancer/Preprocessing.ipynb @@ -98,7 +98,7 @@ }, "outputs": [], "source": [ - "def create_tile_generator(slide, tile_size=1024, overlap=0):\n", + "def create_tile_generator(slide, tile_size, overlap):\n", " \"\"\"\n", " Create a tile generator for the given slide.\n", " \n", @@ -183,7 +183,7 @@ }, "outputs": [], "source": [ - "def process_slide(slide_num, folder, training, tile_size=1024, overlap=0):\n", + "def process_slide(slide_num, folder, training, tile_size, overlap):\n", " \"\"\"\n", " Generate all possible tile indices for a whole-slide image.\n", " \n", @@ -279,7 +279,7 @@ }, "outputs": [], "source": [ - "def keep_tile(tile_tuple, tile_size=1024, tissue_threshold=0.9):\n", + "def keep_tile(tile_tuple, tile_size, tissue_threshold):\n", " \"\"\"\n", " Determine if a tile should be kept.\n", " \n", @@ -345,7 +345,7 @@ }, "outputs": [], "source": [ - "def process_tile(tile_tuple, sample_size=256, grayscale=False):\n", + "def process_tile(tile_tuple, sample_size, grayscale):\n", " \"\"\"\n", " Process a tile into a group of smaller samples.\n", " \n", @@ -633,8 +633,9 @@ "\n", "# Settings\n", "training = True\n", - "sample_size=64\n", - "grayscale = True\n", + "tile_size = 1024\n", + "sample_size = 256\n", + "grayscale = False\n", "num_partitions = 20000\n", "folder = \"/home/MDM/breast_cancer/data\"" ] @@ -648,7 +649,7 @@ "outputs": [], "source": [ "# Process all slides\n", - "df = preprocess(slide_nums, sample_size=sample_size, grayscale=grayscale,\n", + "df = preprocess(slide_nums, tile_size=tile_size, sample_size=sample_size, grayscale=grayscale,\n", " training=training, num_partitions=num_partitions, folder=folder)\n", "df" ] http://git-wip-us.apache.org/repos/asf/incubator-systemml/blob/a11374b8/projects/breast_cancer/README.md ---------------------------------------------------------------------- diff --git a/projects/breast_cancer/README.md b/projects/breast_cancer/README.md index fc1ec0d..dbb626f 100644 --- a/projects/breast_cancer/README.md +++ b/projects/breast_cancer/README.md @@ -131,7 +131,7 @@ References: ## Create a Histopath slide âlabâ to view the slides (just driver): - `git clone https://github.com/openslide/openslide-python.git` - Host locally: - - `python3 path/to/openslide-python/examples/deepzoom/deepzoom_multiserver.py path/to/data/` + - `python3 path/to/openslide-python/examples/deepzoom/deepzoom_multiserver.py -Q 100 path/to/data/` - Host on server: - - `python3 path/to/openslide-python/examples/deepzoom/deepzoom_multiserver.py -l HOSTING_URL_HERE path/to/data/` + - `python3 path/to/openslide-python/examples/deepzoom/deepzoom_multiserver.py -Q 100 -l HOSTING_URL_HERE path/to/data/` - Open local browser to `HOSTING_URL_HERE:5000`.
