Command-line tool: `tda4j`

sbt assembly builds a jar that runs as a command-line tool:

java -jar target/out/jvm/scala-3.9.0/tda4j/tda4j-<version>-assembly.jar [options] <input-file>

It reads a point cloud, distance matrix, image or relation, computes persistence with the same code as the MATLAB interface, and writes the diagram. --help lists every flag; they mirror the MATLAB options one to one:

input and output: --input-format (csv-points, distance-matrix and image formats, csv-relation), --output-format (text, csv, gudhi, dipha, perseus), --output, --representatives (also print each bar's representative);
the computation: --complex, --engine, --max-dimension, --max-filtration-value, --field, --prime, --edge-collapse, --alpha-backend, --require-valid-triangulation, --dtm-k, --dtm-q, --dtm-p, --sparse-epsilon, --dual (relations), --sublevel and --nan-mask (images: --nan-mask false makes a NaN pixel an error instead of a masked one);
the witness complex: --num-landmarks, --witness-variant, --landmark-selector, --landmark-seed, --nu, and the two-step --select-landmarks / --landmarks-file (see witness complexes);
which bars: --min-persistence, --min-persistence-fraction, --include-zero-length; and which representatives: --representative-type (cycles or cocycles);
comparing: --distance-to saved-diagram (with --distance-format, --distance-order, --distance-ground-norm) prints the bottleneck and Wasserstein distances per dimension to a diagram saved earlier, instead of a diagram;
plots: --plot (barcode, diagram, representative, input, complex, landscape, persistence-image, input-3d, complex-3d, representative-3d) draws the result instead of writing it, into --output (.svg or .html) or a page opened in the browser; --bar, --dimension and --at choose what (see plotting);
saved results: --save-result result.json also saves the whole result (bars, representatives, input). The saved file is an input of its own (--input-format result, chosen by itself for such a file): print, convert, compare or plot it without computing again. Computation flags are refused for it.

java -jar tda4j-assembly.jar --max-dimension 1 points.csv
java -jar tda4j-assembly.jar --input-format csv-relation --dual true relation.csv
java -jar tda4j-assembly.jar --max-dimension 1 --save-result circle.json points.csv
java -jar tda4j-assembly.jar --plot representative --output loop.svg circle.json
java -jar tda4j-assembly.jar --output-format gudhi --output circle.pers circle.json

Which bars are reported

As in MATLAB, bars whose persistence is at most 1% of the input's scale are not printed; essential bars always are. When bars were hidden, one line on standard error says how many:

tda4j: 3 bar(s) with persistence <= 0.0195 not reported (58 reported); pass --min-persistence 0 to report them

--min-persistence-fraction changes the 1%, --min-persistence sets an absolute threshold (give at most one; 0 prints every bar). Zero-length bars are only computed with --include-zero-length true. The threshold flags are rejected with --select-landmarks (no diagram) and --distance-to (distances always use every bar).