Allow images/ to be missing for spatial_experiments with no images. (#39

)

CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.24)
 
 project(takane
-    VERSION 0.7.0
+    VERSION 0.7.1
     DESCRIPTION "ArtifactDB file validators"
     LANGUAGES CXX)
 

README.md

@@ -71,7 +71,8 @@ Currently, **takane** provides validators for the following objects:
   [1.0](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/single_cell_experiment/1.0.md).
 - `spatial_experiment`:
   [1.0](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/spatial_experiment/1.0.md),
-  [1.1](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/spatial_experiment/1.1.md).
+  [1.1](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/spatial_experiment/1.1.md),
+  [1.2](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/spatial_experiment/1.2.md).
 - `string_factor`:
   [1.0](https://github.com/ArtifactDB/takane/tree/gh-pages/docs/specifications/string_factor/1.0.md).
 - `summarized_experiment`:

docs/specifications/_build.R

@@ -4,7 +4,7 @@ listings <- list.files(pattern="\\.Rmd$")
 default <- "1.0"
 known.variants <- list(
     simple_list.Rmd="1.1",
-    spatial_experiment.Rmd="1.1"
+    spatial_experiment.Rmd=c("1.1", "1.2")
 )
 
 dest <- "compiled"

docs/specifications/spatial_experiment.Rmd

@@ -37,7 +37,7 @@ The array should be two-dimensional and the extent of the first dimension should
 The extent of the second dimension should be either 2 or 3.
 Each row of the dense array contains the spatial x/y(/z) coordinates of the corresponding sample in the spatial experiment.
 
-The directory should contain an `images` subdirectory, which in turn contains a `mapping.h5` HDF5 file.
+The directory may contain an `images` subdirectory, which in turn contains a `mapping.h5` HDF5 file.
 This file should contain a `spatial_experiment` group, which contains the following children:
 
 - `sample_names`, a 1-dimensional string dataset containing sample names.
@@ -94,6 +94,12 @@ Each image file should start with the magic numbers for its expected format.")
 }
 ```
 
+```{r, results="asis", echo=FALSE}
+if (.version >= package_version("1.2")) {
+cat("Alternatively, the `images` directory may be absent, in which case the `spatial_experiment` is assumed to have no images.")
+}
+```
+
 ## Height
 
 The height of the `spatial_experiment` is defined in the same manner as that of the underlying [`summarized_experiment`](../summarized_experiment).

include/takane/spatial_experiment.hpp

@@ -112,6 +112,11 @@ inline void validate_image(const std::filesystem::path& path, size_t i, const st
 
 inline void validate_images(const std::filesystem::path& path, size_t ncols, Options& options, const ritsuko::Version& version) {
     auto image_dir = path / "images";
+    if (!std::filesystem::exists(image_dir)) {
+        // No images at all, which is permitted.
+        return;
+    }
+
     auto mappath = image_dir / "mapping.h5";
     auto ihandle = ritsuko::hdf5::open_file(mappath);
     auto ghandle = ritsuko::hdf5::open_group(ihandle, "spatial_experiment");

tests/src/spatial_experiment.cpp

@@ -139,6 +139,16 @@ TEST_F(SpatialExperimentTest, ColumnSamples) {
     expect_error("equal the number of columns");
 }
 
+TEST_F(SpatialExperimentTest, NoImages) {
+    spatial_experiment::Options options(20, 19);
+    options.num_samples = 3;
+    options.num_images_per_sample = 0;
+    spatial_experiment::mock(dir, options);
+    std::filesystem::remove_all(dir / "images");
+    EXPECT_FALSE(std::filesystem::exists(dir / "images"));
+    test_validate(dir); 
+}
+
 TEST_F(SpatialExperimentTest, ImageSamples) {
     spatial_experiment::Options options(20, 19);
     options.num_samples = 3;