Texture metamers

.gitignore

@@ -95,4 +95,8 @@ scratch.ipynb
 stimuli.mat
 
 # svg images
-*.svg
+*.svg
+
+# the directories containing outputs
+Kay2013_comparison/
+Metamer_images/

Makefile

@@ -3,68 +3,108 @@ SHELL := /bin/bash
 # for all full stimuli, use the following:
 STIMULI_IDX_full = $(shell seq 69 224)
 
+# for testing:
+# STIMULI_IDX_full := $(shell seq 69 73)
+
 # for all sweep stimuli, use the following (and honestly, this is
 # small enough that you don't need to use something else for testing)
 STIMULI_IDX_sweep = $(shell seq 0 33)
 
-# for testing:
-# STIMULI_IDX_full := $(shell seq 69 73)
+VOXEL_IDX = $(shell seq 0 3)
 
-VOXEL_IDX = $(shell seq 0 9)
+# these defaults are probably fine
+BRODATZ_METAMER_IDX = $(shell seq 1 15)
+FREEMAN2013_METAMER_IDX = $(shell seq 1 15)
+IMAGENET_METAMER_IDX = $(shell seq 1 20)
+NUM_SCALES=4
+NUM_ORIENTATIONS=4
+SIZE_NEIGHBORHOOD=7
+METAMER_SEEDS = $(shell seq 1 5)
 
-# KNK_PATH=/home/billbrod/Documents/Kendrick-socmodel/code/
-KNK_PATH=/Users/winawerlab/matlab/git/knkutils/
+# these you probably need to change
+KNK_PATH=~/matlab/git/knkutils/
 SUBJ=test-sub
 SUBJ_DIR=/Volumes/server/Freesurfer_subjects
-# SUBJ_DIR=/home/billbrod/Documents/SCO-test-data/Freesurfer_subjects
+TEXTURE_SYNTH_PATH=~/matlab/git/textureSynth/
+PYR_TOOLS_PATH=~/matlab/git/matlabPyrTools-master
+
 
 # make sure matlab is in your path, which it may not be by default if you're on Mac.
 
 # for our stimuli, we use the pictures from Kay2013, which Kendrick
 # provides on his website.
-full_stimuli.mat : 
-	wget -q http://kendrickkay.net/socmodel/stimuli.mat -O ./full_stimuli.mat
+Kay2013_comparison :
+	mkdir $@
+
+Kay2013_comparison/full_stimuli.mat : Kay2013_comparison
+	wget -q http://kendrickkay.net/socmodel/stimuli.mat -O ./Kay2013_comparison/full_stimuli.mat
         # we need to do this to get the stimuli.mat into the format we want
 	matlab -nodesktop -nodisplay -r "load('$@','images'); save('$@','images'); quit"
 
-sweep_stimuli.mat : full_stimuli.mat
-	python2.7 pRF_check.py $< {}_stimuli.mat
+Kay2013_comparison/sweep_stimuli.mat : Kay2013_comparison/full_stimuli.mat
+	python2.7 pRF_check.py $< Kay2013_comparison/{}_stimuli.mat
+
+Metamer_images :
+	mkdir $@
+
+# primarily using Freeman 2013 stimuli now, so this might not be relevant.
+Metamer_images/Original_Brodatz_seed_images : Metamer_images
+	wget -q http://multibandtexture.recherche.usherbrooke.ca/images/Original_Brodatz.zip -O ./Original_Brodatz.zip
+	unzip ./Original_Brodatz.zip -d Metamer_images
+	mv Metamer_images/Original\ Brodatz Metamer_images/Original_Brodatz_seed_images
+	rm Original_Brodatz.zip
+
+Metamer_images/Brodatz_metamers : Metamer_images/Original_Brodatz_seed_images/
+	mkdir $@
+	matlab -nodesktop -nodisplay -r "createMetamers('$(TEXTURE_SYNTH_PATH)', '$(PYR_TOOLS_PATH)', '$(KNK_PATH)','$</*.gif', '$@', [$(BRODATZ_METAMER_IDX)], $(NUM_SCALES), $(NUM_ORIENTATIONS), $(SIZE_NEIGHBORHOOD), 20, 5); quit;"
+
+Metamer_images/Freeman2013_seed_images : Metamer_images
+	wget -q https://files.osf.io/v1/resources/9bxut/providers/osfstorage/589e2fa06c613b01f7b350a2/?zip= -O ./Freeman2013.zip
+	jar xvf ./Freeman2013.zip
+	mkdir $@
+	mv tex*im*png $@
+	rm Freeman2013.zip
+
+Metamer_images/Freeman2013_metamers : Metamer_images/Freeman2013_seed_images/
+	mkdir $@
+	matlab -nodesktop -nodisplay -r "createMetamers('$(TEXTURE_SYNTH_PATH)', '$(PYR_TOOLS_PATH)', '$(KNK_PATH)','$</tex-320x320-im*-smp1.png', '$@', [$(FREEMAN2013_METAMER_IDX)], $(NUM_SCALES), $(NUM_ORIENTATIONS), $(SIZE_NEIGHBORHOOD), 20, [$(METAMER_SEEDS)]); quit;"
+
+Metamer_images/ImageNet_seed_images : Metamer_images
+	wget -q https://files.osf.io/v1/resources/9bxut/providers/osfstorage/589e2f98594d9001fa121288/?zip= -O ./ImageNet.zip
+	jar xvf ./ImageNet.zip
+	mkdir $@
+	mv im*png $@
+	mv im*JPEG $@
+	rm ImageNet.zip
+
+Metamer_images/ImageNet_metamers : Metamer_images/ImageNet_seed_images/
+	mkdir $@
+	matlab -nodesktop -nodisplay -r "createMetamers('$(TEXTURE_SYNTH_PATH)', '$(PYR_TOOLS_PATH)', '$(KNK_PATH)','$</im*', '$@', [$(IMAGENET_METAMER_IDX)], $(NUM_SCALES), $(NUM_ORIENTATIONS), $(SIZE_NEIGHBORHOOD), 20, [$(METAMER_SEEDS)]); quit;"
 
 # this will also create soc_model_params_%_image_names.mat in the same call
-soc_model_params_%.csv : %_stimuli.mat
+Kay2013_comparison/soc_model_params_%.csv : Kay2013_comparison/%_stimuli.mat
 	python2.7 model_comparison_script.py $< $(SUBJ) $@ $(STIMULI_IDX_$*) -v $(VOXEL_IDX) -s $(SUBJ_DIR)
 
-voxel_idx.txt :
-	#  we don't need to increment these voxel indices because this
-	#  refers to actual values in the dataframe / table
-	echo $(VOXEL_IDX) > $@
-
-%_stim_idx.txt :
-	echo $(STIMULI_IDX_$*) > $@
-	# for stimuli indices, we need to increment them by one to
-	# turn them from python into matlab indices.
-	python2.7 sco/model_comparison/py_to_matlab.py -p2m $@
-
-MATLAB_soc_model_params_%.csv : soc_model_params_%.csv voxel_idx.txt %_stim_idx.txt 
-	matlab -nodesktop -nodisplay -r "cd $(shell pwd)/sco/model_comparison; compareWithKay2013('$(KNK_PATH)', '$(shell pwd)/$*_stimuli.mat', '$(shell pwd)/$*_stim_idx.txt', '$(shell pwd)/voxel_idx.txt', '$(shell pwd)/$<', '$(shell pwd)/soc_model_params_$*_image_names.mat', '$(shell pwd)/$@'); quit;"
+Kay2013_comparison/MATLAB_soc_model_params_%.csv : Kay2013_comparison/soc_model_params_%.csv
+        # we increment the stimuli index and not the voxel index,
+        # because the voxel indices refer to a column in the
+        # dataframe/table, while the stimuli indices will actually be
+        # used to grab something from an array in matlab
+	matlab -nodesktop -nodisplay -r "cd $(shell pwd)/sco/model_comparison; compareWithKay2013('$(KNK_PATH)', '$(shell pwd)/Kay2013_comparison/$*_stimuli.mat', [$(STIMULI_IDX_$*)]+1, [$(VOXEL_IDX)], '$(shell pwd)/$<', '$(shell pwd)/Kay2013_comparison/soc_model_params_$*_image_names.mat', '$(shell pwd)/$@'); quit;"
 
 .PHONY : %_images
 # this will create several images, with names based on the default options in sco/model_comparison/core.py
-%_images : MATLAB_soc_model_params_%.csv %_stimuli.mat soc_model_params_%.csv
-	python2.7 sco/model_comparison/core.py $* $< soc_model_params_$*_image_names.mat sco/model_comparison/stimuliNames.mat $*_stimuli.mat $(STIMULI_IDX_$*)
-
-.PHONY : cleantmps
-cleantmps :
-	-rm voxel_idx.txt
-	-rm stim_idx.txt
+%_images : Kay2013_comparison/MATLAB_soc_model_params_%.csv Kay2013_comparison/%_stimuli.mat Kay2013_comparison/soc_model_params_%.csv
+	python2.7 sco/model_comparison/core.py $* $< Kay2013_comparison/soc_model_params_$*_image_names.mat sco/model_comparison/stimuliNames.mat Kay2013_comparison/$*_stimuli.mat $(STIMULI_IDX_$*)
+	mv SCO_model_comparison*.svg Kay2013_comparison/
 
 .PHONY : %clean
-%clean : cleantmps
-	-rm soc_model_params_$*.csv
-	-rm soc_model_params_$*_image_names.mat
-	-rm MATLAB_soc_model_params_$*.csv
-	-rm soc_model_params_$*_results_dict.pkl
+%clean : 
+	-rm Kay2013_comparison/soc_model_params_$*.csv
+	-rm Kay2013_comparison/soc_model_params_$*_image_names.mat
+	-rm Kay2013_comparison/MATLAB_soc_model_params_$*.csv
+	-rm Kay2013_comparison/soc_model_params_$*_results_dict.pkl
 
 # this way these won't be deleted as unnecessary intermediates. These
 # take a while to make, so we don't want to do that.
-.PRECIOUS : soc_model_params_%.csv MATLAB_soc_model_params_%.csv
+.PRECIOUS : Kay2013_comparison/soc_model_params_%.csv Kay2013_comparison/MATLAB_soc_model_params_%.csv Kay2013_comparison/full_stimuli.mat