feat: tests

.gitignore

@@ -5,4 +5,10 @@
 .virtualenv
 *.tar
 *.zip
-data/
+data/
+.venv/
+uv.lock
+*egg-info/
+# make sentinel files
+.test
+.format

Makefile

@@ -0,0 +1,31 @@
+.SUFFIXES:
+# phony runners, but actual sentinel files so only rerun when needed
+.PHONY: test format
+test: .test
+format: .format
+
+SHELL := /usr/bin/bash
+PYTHON ?= python3
+PYTHON_FILES=$(wildcard *.py tests/*py tests/helpers/*.py)
+
+.ONESHELL: # source in same shell as pytest
+.test: $(PYTHON_FILES) single-shot.sh | .venv/
+	source .venv/bin/activate
+	$(PYTHON) -m pytest tests | tee $@
+
+# don't format all. Would be a big git revision
+.format: $(wildcard test/*py tests/helpers/*.py) #$(PYTHON_FILES)
+	isort $? | tee $@
+	black $? | tee -a $@
+
+# if we don't have .venv, make it and install this package
+# use 'uv' if we have it
+.ONESHELL:
+.venv/:
+	if command -v uv; then
+		uv venv .venv;
+		uv pip install -e .[dev];
+	else
+	  $(PYTHON) -m venv .venv/;
+	  $(PYTHON) -m pip install -e  .[dev];
+	fi

pyproject.toml

@@ -0,0 +1,29 @@
+[project]
+name = "python-ismrmrd-server"
+version = "0.1.0"
+description = "MRD client/server pair and MRD format convertion utilities"
+readme = "readme.md"
+requires-python = ">=3.12"
+dependencies = [
+    "ismrmrd>=1.14.2",
+    "matplotlib>=3.10.7",
+    "numpy>=2.3.4",
+    "pydicom>=3.0.1",
+]
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "black",
+    "isort",
+]
+[tool.setuptools.packages.find]
+# Include all packages found under "src"
+include = ["*py"]
+# Exclude tests and docs directories
+exclude = ["docker", "*sh", "tests/"]
+
+[pytest]
+tmp_path_retention_count = 1
+
+[tool.pytest.ini_options]
+norecursedirs = "tests/helpers"

single-shot.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+#
+# fork the server for a single shot client call
+# use enviornment to adjust parameters
+# 
+
+
+PORT=${PORT:-9002}
+INFILE=${INFILE:-in/example.h5}
+OUTFILE=${OUTFILE:-/tmp/examle.h5}
+CONFIG=${CONFIG:-invertcontrast}
+OUTGROUP=${OUTGROUP:-dataset} # ismrmr's default
+
+scriptdir="$(cd $(dirname "$0"); pwd)"
+
+# Make output directory if needed
+mkdir -p "$(dirname "$OUTFILE")"
+
+python $scriptdir/main.py -p $PORT &
+pid_server=$!
+python $scriptdir/client.py "$INFILE" -p $PORT -o "$OUTFILE" -c $CONFIG -G "$OUTGROUP"
+
+kill $pid_server
+wait $pid_server
+

tests/helpers/__init__.py

@@ -0,0 +1,66 @@
+import sys
+
+import ismrmrd
+import numpy as np
+import pydicom
+import pydicom.data
+
+import dicom2mrd
+
+MAX = 4095  # 12-bit data
+
+
+def checkers(nz, ny, nx):
+    checker_data = np.zeros((nz,ny, nx), dtype=np.uint16)
+    for z in range(nz):
+        for y in range(ny):
+            for x in range(nx):
+                if (x + y + z) % 2 == 0:
+                    checker_data[z, y, x] = MAX
+                else:
+                    checker_data[z, y, x] = 0
+    return checker_data
+
+
+def write_example(data, outdir, series_number=1):
+    """
+    Write example data files in mdr.h5 and dicom/ formats
+    :param outdir: where to save, likely `tmp_path` from pytest
+    :param series_number: dicom header information
+    :returns: dict with 'mrd' and 'dcmdir' keys
+    """
+    mrd_h5 = outdir / "checker.h5"
+
+    ds = pydicom.dcmread(pydicom.data.get_testdata_file("MR_small.dcm"))
+
+    #ds.PixelData = checkers(ds.NumberOfFrames,ds.Columns,ds.Rows).tobytes()
+    ds.PixelData = data.tobytes()
+    (ds.NumberOfFrames, ds.Columns, ds.Rows) = data.shape
+    ds.SeriesDescription = "Test Checkerboard"
+    ds.MagneticFieldStrength = 1.5
+    ds.AcquisitionTime = "120000.000000"
+    ds.SeriesNumber = series_number
+
+    # Create temporary DICOM folder and file
+    temp_dicom_dir = outdir / "temp_dicoms"
+    temp_dicom_dir.mkdir()
+    temp_dicom = temp_dicom_dir / "temp.dcm"
+    ds.save_as(temp_dicom)
+
+    # 3. use dicom2mrd to make a mrd h5 file
+    args = dicom2mrd.argparse.Namespace(
+        folder=temp_dicom_dir, outFile=mrd_h5, outGroup="dataset"
+    )
+    dicom2mrd.main(args)
+
+    return {'mrd': mrd_h5, 'dcmdir': temp_dicom_dir}
+
+
+def mrd_data(filename, group="dataset"):
+    """Read MRD image data from file"""
+    dataset = ismrmrd.Dataset(filename, group, False)
+
+    # Check what image groups are available
+    dataset_list = dataset.list()
+    image_groups = [name for name in dataset_list if name.startswith("image")]
+    return np.squeeze(dataset.read_image(image_groups[0], 0).data)

tests/test_invert.py

@@ -0,0 +1,23 @@
+import os
+
+import numpy as np
+from helpers import MAX, mrd_data, checkers, write_example
+
+
+def test_invert(tmp_path):
+    data = checkers(4,4,4)
+    examples = write_example(data, tmp_path)
+    in_file = examples["mrd"]
+    out_file = tmp_path / "out.h5"
+
+    os.environ["INFILE"] = str(in_file)
+    os.environ["OUTFILE"] = str(out_file)
+    os.system("./single-shot.sh")
+
+    # Read mrd files and extract numpy matrix
+    in_data = mrd_data(in_file)
+    out_data = mrd_data(out_file)
+    abs_diff = np.abs(out_data - in_data)
+    assert in_data[0, 0, 0] == MAX, "input as expected is 0"
+    assert out_data[0, 0, 0] == 0, "output is inverted"
+    assert np.all(abs_diff == MAX), "all voxels inverted"