Merge pull request #111 from brianqiu/dev2

new data pull in & validate

data/Makefile

@@ -1,35 +1,17 @@
 data:
 	wget http://openfmri.s3.amazonaws.com/tarballs/ds005_raw.tgz
-<<<<<<< HEAD
-
+	wget http://nipy.bic.berkeley.edu/rcsds/ds005_mnifunc.tar
+	wget http://nipy.bic.berkeley.edu/rcsds/mni_icbm152_nlin_asym_09c_2mm.tar.gz
+
 validate:
 	python data.py
 
 unzip:
 	tar -xvzf ds005_raw.tgz 
-	for i in {1..9}
-	do
-	for j in {1..3}
-	do
-	gunzip ds005/sub00${i}/BOLD/task001_run00${j}/bold.nii.gz
-	done
-	done
-
-	for i in {10..16}
-	do
-	for j in {1..3}
-	do
-	gunzip ds005/sub0${i}/BOLD/task001_run00${j}/bold.nii.gz
-	done
-	done
-
-=======
-	tar -xvzf ds005_raw.tgz
-	#wget http://nipy.bic.berkeley.edu/rcsds/ds005_mnifunc.tar
-	#tar -xvf ds005_mnifunc.tar
+	tar -xvf ds005_mnifunc.tar
+	tar -xvzf mni_icbm152_nlin_asym_09c_2mm.tar.gz
 	rm ds005_raw.tgz
-	#rm ds005_mnifunc.tar
-
-validate:
-	python data.py	
->>>>>>> a96098ccbb47c304f972e54f9161165806dc04f1
+	rm ds005_mnifunc.tar
+	rm mni_icbm152_nlin_asym_09c_2mm.tar.gz
+	mv mni_icbm152_nlin_asym_09c_2mm templates
+	mv templates/mni_icbm152_t1_tal_nlin_asym_09c_2mm.nii templates/mni_standard.nii

data/README.md

@@ -0,0 +1,18 @@
+The ds005 dataset, filtered ds005 dataset, and mni templates are stored here. Th
+e makefile is written such that:
+
+- 'make data' will pull in the appropriate data 
+- 'make unzip' will unzip, remove, and rename certain files
+- 'make validate' will run data.py to check the hashes of each downloaded file w
+ith a master hashlist included, ensuring all downloaded data is correct  
+
+THE COMMANDS SHOULD BE DONE IN THIS ORDER to be successfully validated. The ds00
+5 folder contains subfolders for each subject, the most relevant of which are:
+
+- BOLD: raw data of fMRI scans for each of the subjects three runs, as well as d
+isplacement/variance data 
+- behav: file for each run that contains the onsets, potential gains, potential 
+losses, and response of each trial
+- model: filtered, processed data of fMRI scans for each of the subjects three r
+uns, and the onsets files
+-

data/data.py

@@ -1,5 +1,4 @@
 from __future__ import print_function, division
-import os
 import hashlib
 import json
 
@@ -48,8 +47,7 @@ def check_hashes(d):
     ex: make_hash_list("ds005", "temp") makes hashlist for all of ds005
     including subdirectories
     """
-
-"""
+    """
     file_paths = []
     for path, subdirs, files in os.walk(directory):
         for name in files:
@@ -58,12 +56,9 @@ def check_hashes(d):
     with open(title, 'w') as outfile:
         json.dump(dictionary, outfile)
     return dictionary
-"""
+    """
 
 if __name__ == "__main__":
-    with open('hashList.txt', 'r') as hl:
+    with open('total_hash.txt', 'r') as hl:
         d = json.load(hl)
     check_hashes(d)
-    #with open('new_hashList.txt', 'r') as hl2:
-    #    data = json.load(hl2)
-    #check_hashes(data)