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Posted to commits@systemml.apache.org by du...@apache.org on 2017/02/06 22:50:17 UTC
incubator-systemml git commit: [SYSTEMML-1185] Minor updates to the
breast cancer project.
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 <mw...@us.ibm.com>
Authored: Mon Feb 6 14:48:12 2017 -0800
Committer: Mike Dusenberry <mw...@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 \u201clab\u201d 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`.