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Kevin Mader kmader

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kmader / 0-Overview.md
Last active March 21, 2017 08:56
KNIME DICOM Reading Issue

Loading Issue

I think the image loading problem is related to the 'Load group files' checkbox, if you leave it unchecked it seems to work fine.

The error message is:

ERROR Image Reader         3:38       Execute failed: Encountered duplicate row ID  "/Users/mader/Documents/TCGA_DICOMS/DOI/TCGA-17-Z011/1.3.6.1.4.1.14519.5.2.1.7777.9002.119175415668704314181906368452/1.3.6.1.4.1.14519.5.2.1.7777.9002.147921136202653008422021343284/000000.dcm" at row number 3

The test file is attached as 000000.dcm

@kmader
kmader / stage1_labels.csv
Created February 11, 2017 12:47
LSB_LabelData
id cancer
0015ceb851d7251b8f399e39779d1e7d 1
0030a160d58723ff36d73f41b170ec21 0
003f41c78e6acfa92430a057ac0b306e 0
006b96310a37b36cccb2ab48d10b49a3 1
008464bb8521d09a42985dd8add3d0d2 1
0092c13f9e00a3717fdc940641f00015 0
00986bebc45e12038ef0ce3e9962b51a 0
00cba091fa4ad62cc3200a657aeb957e 0
00edff4f51a893d80dae2d42a7f45ad1 1
@kmader
kmader / README.md
Last active January 17, 2017 16:15
DictDialog in pyqt

Overview

Creates a simple dialog box based on a dictionary with various keys like (check, list, and linedit)

@kmader
kmader / Simple_Submission.ipynb
Created December 11, 2016 09:23
A python script for making a submission to the InClass Kaggle competition for Micro and Nano Tomography
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@kmader
kmader / README.md
Last active October 21, 2016 14:58
Important Docker Python Packages

Deep Learning / Tensorflow

# Install Python 3 Tensorflow
RUN conda install --quiet --yes 'tensorflow=0.9.0'
# Keras
RUN conda install --channel https://conda.anaconda.org/KEHANG --quiet --yes 'keras=1.0.8'

Elephas

@kmader
kmader / README.md
Created October 20, 2016 15:22
UNET to KNIME

Goal: Keras to KNIME

Model Conversion

JSON -> KNIME Workflow

The model file is below as a json output.

Weight Importing

Original (better)

Original weights are stored in HDF5

@kmader
kmader / Overview.png
Last active October 19, 2016 18:28
SQL Experiments with KNIME
Overview.png
@kmader
kmader / README.md
Created October 19, 2016 09:30
Excel MashFest

Install Packages

install.packages(c("xlsx", "dplyr", "plyr"))

Combine everything together

xls_files_to_read <- Sys.glob("../TumorSegmentation/*.xlsx")
print(paste(xls_files_to_read, collapse = ", "))
@kmader
kmader / Overview.md
Created October 12, 2016 13:00
Fitting and Running Simple GLM Allstate Models

Fitting the Models

fit_model<-function(in_df) glm(loss~.,
                data = in_df %>% 
                  select(starts_with("cont"), 
                         one_of(keep_cats),
                         loss), 
                family = Gamma(link = "log"))
@kmader
kmader / Extra Packages.md
Created October 7, 2016 17:37
Anaconda Python3 Setup

Standard Image Processing

./conda install --channel https://conda.anaconda.org/menpo tbb
./conda install --channel https://conda.anaconda.org/janc opencv3

Deep Learning

./conda install -c conda-forge tensorflow