ENH: Use cellprofiler batch mode for multi-core processing

Makefile

@@ -8,6 +8,7 @@
 
 # Overwritable paths to executables
 CELLPROFILER := cellprofiler
+PARALLEL := parallel
 PYTHON := python
 RSCRIPT := Rscript
 
@@ -21,8 +22,15 @@ TARGETS_img_filelist := results/cellprofiler/filelist
 SOURCES_cellprofiler_filelist := $(TARGETS_img_filelist)
 SOURCES_cellprofiler_pipe := src/image-processing-pipeline.cpproj
 SOURCES_cellprofiler_img := $(TARGETS_zproj)
-SOURCES_cellprofiler := $(SOURCES_cellprofiler_filelist) \
-	$(SOURCES_cellprofiler_pipe) $(SOURCES_cellprofiler_img)
+SOURCES_cellprofiler_common := $(SOURCES_cellprofiler_filelist)	\
+	$(SOURCES_cellprofiler_img)
+SOURCES_cellprofiler_gui := $(SOURCES_cellprofiler_common)	\
+	$(SOURCES_cellprofiler_pipe)
+SOURCES_cellprofiler_batch := $(SOURCES_cellprofiler_common)
+TARGETS_cellprofiler_batch := results/cellprofiler/Batch_data.h5
+SOURCES_cellprofiler_commands := $(TARGETS_cellprofiler_batch)
+TARGETS_cellprofiler_commands := results/cellprofiler/batch_commands.sh
+SOURCES_cellprofiler_headless := $(TARGETS_cellprofiler_commands)
 TARGETS_cellprofiler_db := results/cellprofiler/all-plates.db
 TARGETS_cellprofiler_prop := results/cellprofiler/all-plates.properties
 TARGETS_cellprofiler := $(TARGETS_cellprofiler_db) $(TARGETS_cellprofiler_prop)
@@ -70,7 +78,13 @@ $(TARGETS_img_zproj) : $(SOURCES_img_zproj)
 
 .PHONY : cellprofiler
 cellprofiler : $(TARGETS_cellprofiler) ## Collect statistics about all images.
-$(call singleton,$(TARGETS_cellprofiler)) : $(SOURCES_cellprofiler)
+$(call singleton,$(TARGETS_cellprofiler)) : $(SOURCES_cellprofiler_headless)
+	$(PARALLEL) :::: $<
+
+$(TARGETS_cellprofiler_commands) : $(SOURCES_cellprofiler_commands)
+	$(CELLPROFILER) --get-batch-commands=$< | sed 's#^CellProfiler#$(CELLPROFILER)#' > $@
+
+$(TARGETS_cellprofiler_batch) : $(SOURCES_cellprofiler)
 	$(CELLPROFILER) $(CELLPROFILER_OPTS) --run-headless
 
 .PHONY : gui-cellprofiler