tm.snkmk

from string import Template


## needs to be passed by command line
##movie="PA_Sample_NoCorrection"
##movieDbDir="/projects/project-raphael/movie_dbs/db_tests/copy_test/PA_Sample_NoCorrection"
##movieDbDir=config["movie_dir"]

## todo test if movie_dir is present in config array and use instead
movieDbDir=os.path.abspath('.')

movie = os.path.basename(movieDbDir)

DB = movie + ".sqlite"
T1_COUNTS = "topochanges/topoChangeSummary.RData"
TRACKED_ROIS = "roi_bt/lgRoiSmoothed.RData"
TRIANGLES = "shear_contrib/triList.RData"

# https://bitbucket.org/johanneskoester/snakemake/wiki/Documentation#markdown-header-local-rules
localrules: parse_tables, make_db

## grep output /projects/project-raphael/scripts/tissue_miner/workflow/tm.snkmk | tail -n+2 | cut -d: -f2-  | sort -u | tr "\\n" ","
rule all:
    input:  "4way_vertices/not3_vertices.mp4", DB, "dbTablesFromParser/vertex_in_frame.dat", "lg_color_optimization/lg_colors.txt", "lineage/generation_limit_range.mp4", "nematics_movies/" + movie + "_cell_elongation.mp4", "polygon_class/polygon_class_discrete.mp4", "shear_contrib/thirdInt.RData", TRIANGLES, "state_movies/" + movie + "_cell_area_rainbow.mp4", "state_movies/" + movie + "_DBelong_nematics.mp4", "state_movies/" + movie + "_cell_elong_norm.mp4", "stripe_movies/blue_square_tracking.mp4", T1_COUNTS, "topochanges/t1_balance_smoothed.mp4", "topochanges/t1_rates_smoothed.mp4", TRACKED_ROIS, "tri_categories/triangleCategories.RData", "roi_bt/corrected_border.mp4", "shear_contrib/raw/Ta_t.RData"


# rule hello:
#     run:
#         print(vars())
#
#


## merged into CreateDbFromParser for convenience and better readability
#rule rotate_originals:
#    shell: "RotateOriginals.sh"  + movieDbDir

rule prepare_movie:
    params: name="prepare_movie"
    output: "Segmentation/movieInformation.dat"
    #shell: "CreateMovieInfoDat.sh "  + movieDbDir 
	shell: "PrepareDataForParser.sh " + movieDbDir # also generate original.png needed by the parser 


rule parse_tables:
    params: name="parse_tables"
    input: "Segmentation/movieInformation.dat"
    output: "dbTablesFromParser/vertex_in_frame.dat"
    # shell: Template("/sw/bin/xvfb-run imageParser $(dirname $movieDbDir) $(basename $movieDbDir)  %03d").safe_substitute(vars())
#    shell: "/sw/bin/xvfb-run imageParser $(dirname {movieDbDir}) $(basename {movieDbDir}) %03d" #optionally remove tracked and divided pngs
    shell: "imageParser $(dirname {movieDbDir}) $(basename {movieDbDir}) %03d" #optionally remove tracked and divided pngs


rule make_db:
    params: name="make_db"
    input: "dbTablesFromParser/vertex_in_frame.dat", "Segmentation/cumultimesec.txt"
    output: DB, "cellshapes.RData"
    shell: "CreateDbFromParser.R "  + movieDbDir

# shell: "$TM_HOME/db/movie_rotation/RotateOriginals.sh " + movieDbDir +" ; CreateDbFromParser.R "  + movieDbDir

rule roi_tracking:
    params: name="roi_tracking"
    input: DB
    output: TRACKED_ROIS
    shell: "UserRoiTracking.R "  + movieDbDir


rule roi_movies:
    params: name="roi_movies"
    input: TRACKED_ROIS
    output: "roi_bt/corrected_border.mp4"
    shell: "RoiTrackingMovies.R "  + movieDbDir


rule roi_deform:
    params: name="roi_deform"
    input: DB
    shell: "RoiDeformation.R "  + movieDbDir


### Lineage Analysis

rule lineage_colors:
    params: name="lineage_colors"
    input: DB
    output: "lg_color_optimization/lg_colors.txt"
    shell: "LineageGroupColoring.R " + movieDbDir


rule lineage_movies:
    params: name="lineage_movies"
    input: "lg_color_optimization/lg_colors.txt"
    output: "lineage/generation_limit_range.mp4"
    shell: "LineageMovies.R " + movieDbDir


### Topology Analysis



rule topo_countt1:
    params: name="topo_countt1"
    input: DB, TRACKED_ROIS
    output: T1_COUNTS
    shell: "CountT1.R "  + movieDbDir
    
rule topo_movies:
    params: name="topo_movies"
    input: T1_COUNTS
    output: "topochanges/t1_rates_smoothed.mp4"
    shell: "TopologyMovies.R "  + movieDbDir


rule topo_unbalance:
    params: name="topo_unbalance"
    input: T1_COUNTS
    output: "topochanges/t1_balance_smoothed.mp4"
    shell: "UnbalanceT1Movie.R "  + movieDbDir


rule four_way:
    params: name="four_way"
    input: DB
    output: "4way_vertices/not3_vertices.mp4"
    shell: "FourWayVertices.R "  + movieDbDir


rule polygon_class:
    params: name="polygon_class"
    input: TRACKED_ROIS
    output: "polygon_class/polygon_class_discrete.mp4"
    shell: "PolygonClass.R " + movieDbDir


## triangles

rule tri_create:
    params: name="tri_create"
    input: DB
    output: TRIANGLES
    shell: "CreateTriangles.R " + movieDbDir

rule tri_categorize:
    params: name="tri_categorize"
    input: T1_COUNTS, TRIANGLES
    output: "tri_categories/triangleCategories.RData"
    ## todo use function here to simplify log creation
    shell: "CategorizeTriangles.R "  + movieDbDir # direct log redirection: + "2>tri_categorize.err.log 1>tri_categorize.out.log"

### misc

rule area_movies:
    params: name="area_movies"
    input: DB
    output: "state_movies/" + movie + "_cell_area_rainbow.mp4"
    shell: "AreaMovies.R " + movieDbDir

rule db_elongation_movies:
    params: name="db_elongation_movies"
    input: DB
    output: "state_movies/" + movie + "_DBelong_nematics.mp4", "state_movies/" + movie + "_cell_elong_norm.mp4"
    shell: "DbElongationMovie.R " + movieDbDir

rule density_movies:
    params: name="density_movies"
    input: DB
    output: "state_movies/cell_density.mp4"
    shell: "DensityMovies.R " + movieDbDir

rule deformation_movies:
    params: name="deformation_movies"
    input: DB
    output: "stripe_movies/blue_square_tracking.mp4"
    shell: "StripeMovies.R " + movieDbDir


### shear

#def redirect_out(ruleName):
#   return " 2>logs/"+ruleName+".err.log 1>logs/"+ ruleName + ".out.log"
## usage: + redirect_out("shear_calculate")

rule shear_calculate:
    params: name="shear_calculate"
    input: TRACKED_ROIS, TRIANGLES
    output: "shear_contrib/thirdInt.RData", "shear_contrib/raw/Ta_t.RData"
    shell: "CalculateShearContributions.R " + movieDbDir

rule shear_movies:
    params: name="shear_movies"
    input: "shear_contrib/thirdInt.RData"
    output: "nematics_movies/" + movie + "_cell_elongation.mp4"
    shell: "NematicsMovies.R " + movieDbDir