MAINT: Rearrange files to comply with http://arxiv.org/abs/1609.00037

.gitignore

@@ -1,9 +1,12 @@
 # Data
-cellprofiler_all-plates.tar.xz
-cellprofiler_all-plates/all-plates.db
-z_stack.tar.xz
-z_stack/
+data/April_14_2016.tar.xz
+data/April_14_2016/
+results/cellprofiler/2017-01-04/cellprofiler_all-plates.tar.xz
+results/cellprofiler/2017-02-20/
+results/z_projection.tar.xz
+results/z_projection/
 *.csv
+*.db
 *.pdf
 *.png
 *.svg
@@ -12,4 +15,6 @@ z_stack/
 *.log
 
 # R
-.Rhistory
+.Rhistory
+.Rproj.user
+*.Rproj

results/cellprofiler/cellprofiler.mk

@@ -0,0 +1,29 @@
+# Behavior: empty values are considered false
+controls_only = yes
+
+# Paths
+PREFIX_OUTPUT = 2017-02-20
+PREFIX_SRC = ../../src
+IMAGES = ../z_projection
+PIPELINE = $(PREFIX_SRC)/image-processing-pipeline.cpproj
+FILELIST = $(PREFIX_OUTPUT)/filelist
+
+# Executables
+cellprofiler = cellprofiler
+
+.PHONY: cellprofiler
+cellprofiler : $(FILELIST)
+	$(cellprofiler) \
+	--pipeline=$(PIPELINE) \
+	--output-directory=$(PREFIX_OUTPUT) \
+	--file-list=$(FILELIST)
+
+.PHONY : filelist
+filelist : $(FILELIST)
+$(FILELIST) : $(IMAGES)
+ifneq ($(CLUSTER),)
+	find $< -type f | sort > $@
+else
+#find $< -type f -regex '^502[^_]_(J18|I09|H09|N22|E20|M13|K11)' | sort > $@
+	find $< -type f -regex '.*/502[^_]+_J18_S08.*' | sort > $@
+endif

src/image_preprocessing_z_projection.py

@@ -0,0 +1,51 @@
+"""
+Reduce image Z-stack to maximum intensity projection.
+"""
+# pylint: disable=invalid-name,superfluous-parens
+
+import glob
+import multiprocessing as mp
+import os
+
+import numpy as np
+import scipy.misc
+
+
+out_dir = "../results/z_projection"
+z_slices = 3
+# Assume all files are tif, and therefore that the number of files is
+# a multiple of z_slices.
+print("Reading file list")
+all_files = glob.glob('../data/April_14_2016/*/*')
+all_files.sort()
+
+if not os.path.exists(out_dir):
+    print("Creating output directory")
+    os.mkdir(out_dir)
+
+print("Creating output file list")
+all_files_out = [
+    os.path.join(out_dir,
+                 os.path.basename(all_files[i].replace("_Z1", "")))
+    for i in xrange(0, len(all_files), z_slices)
+]
+
+def max_projection(pool_index):
+    """
+    Create and save image maximum intensity projection.
+    """
+    offset = pool_index * z_slices
+    im1 = scipy.misc.imread(all_files[offset])
+    shape = [1] + list(im1.shape)
+    for file_ in all_files[offset + 1:offset + z_slices]:
+        im2 = scipy.misc.imread(file_)
+        im_stack = np.concatenate((im1.reshape(shape),
+                                   im2.reshape(shape)), axis=0)
+        im1 = im_stack.max(axis=0)
+    scipy.misc.imsave(all_files_out[pool_index], im1)
+
+print("Reading images, merging and saving (this can take a while)")
+pool = mp.Pool()
+pool.map(max_projection, xrange(len(all_files_out)))
+
+print("Finished")