diff options
Diffstat (limited to 'reproduce/analysis')
| -rw-r--r-- | reproduce/analysis/config/verify-outputs.mk | 3 | ||||
| -rw-r--r-- | reproduce/analysis/make/delete-me.mk | 37 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 11 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 1 | ||||
| -rw-r--r-- | reproduce/analysis/make/verify.mk | 116 |
5 files changed, 146 insertions, 22 deletions
diff --git a/reproduce/analysis/config/verify-outputs.mk b/reproduce/analysis/config/verify-outputs.mk new file mode 100644 index 0000000..5d8eff1 --- /dev/null +++ b/reproduce/analysis/config/verify-outputs.mk @@ -0,0 +1,3 @@ +# To disable verification of output datasets set this variable to yes + +verify-outputs = yes diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index eb6d919..3ba4909 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -23,10 +23,10 @@ # ------------- # # We will use AWK to generate a table showing X and X^2 and draw its plot. -dmdir = $(texdir)/delete-me -dm = $(dmdir)/data.txt -$(dmdir): | $(texdir); mkdir $@ -$(dm): $(pconfdir)/delete-me-num.mk | $(dmdir) +delete-numdir = $(texdir)/delete-me-num +delete-num = $(delete-numdir)/data.txt +$(delete-numdir): | $(texdir); mkdir $@ +$(delete-num): $(pconfdir)/delete-me-num.mk | $(delete-numdir) # When the plotted values are re-made, it is necessary to also # delete the TiKZ externalized files so the plot is also re-made. @@ -44,10 +44,10 @@ $(dm): $(pconfdir)/delete-me-num.mk | $(dmdir) # # For an example image, we'll make a PDF copy of the WFPC II image to # display in the paper. -dddemodir = $(texdir)/delete-me-demo -$(dddemodir): | $(texdir); mkdir $@ -demopdf = $(dddemodir)/wfpc2.pdf -$(demopdf): $(dddemodir)/%.pdf: $(indir)/%.fits | $(dddemodir) +delete-demodir = $(texdir)/delete-me-demo +$(delete-demodir): | $(texdir); mkdir $@ +delete-pdf = $(delete-demodir)/wfpc2.pdf +$(delete-pdf): $(delete-demodir)/%.pdf: $(indir)/%.fits | $(delete-demodir) # When the plotted values are re-made, it is necessary to also # delete the TiKZ externalized files so the plot is also re-made. @@ -64,8 +64,9 @@ $(demopdf): $(dddemodir)/%.pdf: $(indir)/%.fits | $(dddemodir) # ------------------------ # # For an example plot, we'll show the pixel value histogram also. -histogram = $(dddemodir)/wfpc2-hist.txt -$(histogram): $(dddemodir)/%-hist.txt: $(indir)/%.fits | $(dddemodir) +delete-histogram = $(delete-demodir)/wfpc2-hist.txt +$(delete-histogram): $(delete-demodir)/%-hist.txt: $(indir)/%.fits \ + | $(delete-demodir) # When the plotted values are re-made, it is necessary to also # delete the TiKZ externalized files so the plot is also re-made. @@ -83,8 +84,9 @@ $(histogram): $(dddemodir)/%-hist.txt: $(indir)/%.fits | $(dddemodir) # # This is just as a demonstration on how to get analysic configuration # parameters from variables defined in `reproduce/analysis/config/'. -stats = $(dddemodir)/wfpc2-stats.txt -$(stats): $(dddemodir)/%-stats.txt: $(indir)/%.fits | $(dddemodir) +delete-stats = $(delete-demodir)/wfpc2-stats.txt +$(delete-stats): $(delete-demodir)/%-stats.txt: $(indir)/%.fits \ + | $(delete-demodir) aststatistics $< -h0 --mean --median > $@ @@ -98,7 +100,8 @@ $(stats): $(dddemodir)/%-stats.txt: $(indir)/%.fits | $(dddemodir) # # NOTE: In LaTeX you cannot use any non-alphabetic character in a variable # name. -$(mtexdir)/delete-me.tex: $(dm) $(demopdf) $(histogram) $(stats) +$(mtexdir)/delete-me.tex: $(delete-num) $(delete-pdf) $(delete-histogram) \ + $(delete-stats) # Write the number of random values used. echo "\newcommand{\deletemenum}{$(delete-me-num)}" > $@ @@ -112,15 +115,15 @@ $(mtexdir)/delete-me.tex: $(dm) $(demopdf) $(histogram) $(stats) # values, then using it again to read each separately to use in the # macro definition. mm=$$(awk 'BEGIN{min=99999; max=-min} - {if($$2>max) max=$$2; if($$2<min) min=$$2;} - END{print min, max}' $(dm)); + !/^#/{if($$2>max) max=$$2; if($$2<min) min=$$2;} + END{print min, max}' $(delete-num)); v=$$(echo "$$mm" | awk '{printf "%.3f", $$1}'); echo "\newcommand{\deletememin}{$$v}" >> $@ v=$$(echo "$$mm" | awk '{printf "%.3f", $$2}'); echo "\newcommand{\deletememax}{$$v}" >> $@ # Write the statistics of the WFPC2 image as a macro. - mean=$$(awk '{printf("%.2f", $$1)}' $(stats)) + mean=$$(awk '{printf("%.2f", $$1)}' $(delete-stats)) echo "\newcommand{\deletemewfpctwomean}{$$mean}" >> $@ - median=$$(awk '{printf("%.2f", $$2)}' $(stats)) + median=$$(awk '{printf("%.2f", $$2)}' $(delete-stats)) echo "\newcommand{\deletemewfpctwomedian}{$$median}" >> $@ diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index f76f5de..a4eeb2e 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -28,17 +28,18 @@ # `$(mtexdir)/project.tex' is actually just a combination of separate files # that keep the LaTeX macros related to each workhorse Makefile (in # `reproduce/src/make/*.mk'). Those individual macros are pre-requisites to -# `$(mtexdir)/project.tex'. The only workhorse Makefile that doesn't need -# to produce LaTeX macros is this Makefile (`reproduce/src/make/paper.mk'). +# `$(mtexdir)/verify.tex' which will check them before starting to build +# the paper. The only workhorse Makefile that doesn't need to produce LaTeX +# macros is this Makefile (`reproduce/src/make/paper.mk'). # -# This file is thus the interface between the processing scripts and the -# final PDF: when we get to this point, all the processing has been +# This file is thus the interface between the analysis/processing steps and +# the final PDF: when we get to this point, all the processing has been # completed. # # Note that if you don't want the final PDF and just want the processing # and file outputs, you can remove the value of `pdf-build-final' in # `reproduce/analysis/config/pdf-build.mk'. -$(mtexdir)/project.tex: $(foreach s, $(subst paper,,$(makesrc)), $(mtexdir)/$(s).tex) +$(mtexdir)/project.tex: $(mtexdir)/verify.tex # If no PDF is requested, or if LaTeX isn't available, don't # continue to building the final PDF. Otherwise, merge all the TeX diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 27fe16a..0292d3c 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -113,6 +113,7 @@ endif makesrc = initialize \ download \ delete-me \ + verify \ paper diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk new file mode 100644 index 0000000..440ac57 --- /dev/null +++ b/reproduce/analysis/make/verify.mk @@ -0,0 +1,116 @@ +# Verify the project outputs before building the paper. +# +# Copyright (C) 2020 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# +# This Makefile is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# This Makefile is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# A copy of the GNU General Public License is available at +# <http://www.gnu.org/licenses/>. + + + + + +# Verification functions +# ---------------------- +# +# These functions are used by the final rule in this Makefil +verify-print-tips = \ + echo "If you are still developing your project, you can disable"; \ + echo "verification by removing the value of the variable in the"; \ + echo "following file (from the top project source directory):"; \ + echo " reproduce/analysis/config/verify-outputs.mk"; \ + echo; \ + echo "If this is the final version of the file, you can just copy"; \ + echo "and paste the calculated checksum (above) for the file in"; \ + echo "the following project source file:"; \ + echo " reproduce/analysis/make/verify.mk" + +verify-txt-no-comments-leading-space = \ + infile=$(strip $(1)); \ + inchecksum=$(strip $(2)); \ + checksum=$$(sed -e 's/^[[:space:]]*//g' \ + -e 's/\#.*$$//' \ + -e '/^$$/d' $$infile \ + | md5sum \ + | awk '{print $$1}'); \ + if [ x"$$inchecksum" = x"$$checksum" ]; then \ + echo "Verified: $$infile"; \ + else \ + echo; \ + echo "VERIFICATION ERROR"; \ + echo "------------------"; \ + $(call verify-print-tips); \ + echo; \ + echo "Checked file (without empty or commented lines):"; \ + echo " $$infile"; \ + echo "Expected MD5 checksum: $$inchecksum"; \ + echo "Calculated MD5 checksum: $$checksum"; \ + echo; exit 1; \ + fi; + + + + + +# Final verification TeX macro (can be empty) +# ------------------------------------------- +# +# This is the FINAL analysis step (before going onto the paper. Please use +# this step to veryify the contents of the figures/tables used in the paper +# and the LaTeX macros generated from all your processing. It should depend +# on all the LaTeX macro files that are generated (their contents will be +# checked), and any files that go into the tables/figures of the paper +# (generated in various stages of the analysis. +# +# Since each analysis step's data files are already prerequisites of their +# respective TeX macro file, its enough for `verify.tex' to depend on the +# final TeX macro. +# +# USEFUL TIP: during the early phases of your research (when you are +# developing your analysis, and the values aren't final), you can comment +# the respective lines. +# +# Here is a description of the variables defined here. +# +# verify-dep: The major step dependencies of `verify.tex', this includes +# all the steps that must be finished before it. +# +# verify-changes: The files whose contents are important. This is +# essentially the same as `verify-dep', but it has removed +# the `initialize' step (which is information about the +# pipeline, not the results). +verify-dep = $(subst verify,,$(subst paper,,$(makesrc))) +verify-check = $(subst initialize,,$(verify-dep)) +$(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) + + # Make sure that verification is actually requested. + if [ x"$(verify-outputs)" = xyes ]; then + + # Verify the figure datasets. + $(call verify-txt-no-comments-leading-space, \ + $(delete-num), ad345e873e6af577f0e4e7c8942cdf08) + $(call verify-txt-no-comments-leading-space, \ + $(delete-histogram), 12a81c4c8c5f552e5ed5686453587fe8) + + # Verify TeX macros (the values that go into the PDF text). + for m in $(verify-check); do + file=$(mtexdir)/$$m.tex + if [ $$m == delete-me ]; then s=711e2f7fa1f16ecbeeb3df6bcb4ec705 + elif [ $$m == download ]; then s=6749e17ce606d57d30cebdbc1a5d23ad + else echo; echo "'$$m' not recognized."; exit 1 + fi + $(call verify-txt-no-comments-leading-space, $$file, $$s) + done + fi + + # Make an empty final target. + touch $@ |