Merge remote-tracking branch 'upstream/main'

README.md

@@ -3,45 +3,152 @@ Status](https://github.com/ImagingDataCommons/libdicom/actions/workflows/run_uni
 
 # libdicom
 
-C library and executable tools for reading DICOM files.
+libdicom is a C library and a set of command-line tools
+for reading DICOM WSI files. It is free (MIT licensed),
+fast, cross-platform, uses little memory, has no dependencies, [includes API
+documentation](http://www.rollthepotato.net/~john/libdicom/index.html),
+and is [easy to use from languages like
+Python](https://github.com/jcupitt/pylibdicom).
 
-## Getting started
+![A DICOM WSI being viewed via OpenSlide 4.0](data/vipsdisp.png)
 
-### Building from source
+libdicom returns compressed frame data, not RGB pixel arrays. OpenSlide 4.0
+uses libdicom to implement DICOM support and is a better choice if you want
+to process image files.
+
+libdicom aims to support most popular DICOM WSI variants. If you have a
+sample file which does not work well, please [open an issue and we'll try
+to add support](https://github.com/ImagingDataCommons/libdicom/issues).
+
+## Building from source
 
 ```shell
-meson setup --buildtype release builddir
+cd libdicom-1.0.0
+meson setup builddir --buildtype release
 meson compile -C builddir
 meson install -C builddir
 ```
 See [the installation
-documentation](https://libdicom.readthedocs.io/en/latest/installation.html)
+documentation](https:/http://www.rollthepotato.net/~john/libdicom/installation.html)
 for build dependencies and installation options.
 
-### Printing the metadata of a DICOM file
-
-```shell
-dcm-dump data/test_files/sm_image.dcm
+## Sample code
+
+See [the
+documentation](http://www.rollthepotato.net/~john/libdicom/index.html)
+for full details.
+
+```c
+#include <stdlib.h>
+#include <dicom/dicom.h>
+
+int main() {
+    const char *file_path = "/path/to/file.dcm";
+    DcmError *error = NULL;
+
+    DcmFilehandle *filehandle = dcm_filehandle_create_from_file(&error, file_path);
+    if (filehandle == NULL) {
+        dcm_error_log(error);
+        dcm_error_clear(&error);
+        return 1;
+    }
+
+    const DcmDataSet *metadata =
+        dcm_filehandle_get_metadata_subset(&error, filehandle);
+    if (metadata == NULL) {
+        dcm_error_log(error);
+        dcm_error_clear(&error);
+        dcm_filehandle_destroy(filehandle);
+        return 1;
+    }
+
+    const char *num_frames;
+    uint32_t tag = dcm_dict_tag_from_keyword("NumberOfFrames");
+    DcmElement *element = dcm_dataset_get(&error, metadata, tag);
+    if (element == NULL ||
+        !dcm_element_get_value_string(&error, element, 0, &num_frames)) {
+        dcm_error_log(error);
+        dcm_error_clear(&error);
+        dcm_filehandle_destroy(filehandle);
+        return 1;
+    }
+
+    printf("NumerOfFrames == %s\n", num_frames);
+
+    dcm_filehandle_destroy(filehandle);
+
+    return 0;
+}
 ```
 
-### Fetching a frame from a file
+Or in Python:
+
+```python
+import sys
+import pylibdicom
+
+file = pylibdicom.Filehandle.create_from_file(sys.argv[1])
+metadata = file.get_metadata_subset()
+num_frames_tag = pylibdicom.Tag.create_from_keyword("NumberOfFrames")
+num_frames = int(metadata.get(num_frames_tag).get_value()[0])
+for frame_number in range(1, num_frames + 1):
+    frame = file.read_frame(frame_number)
+    value = frame.get_value()
+    print(f"frame {frame_number} -> {frame} {len(value)} bytes")
+
+# you can also read frames by (x, y) tile position ... this works for
+# TILED_FULL and for sparse images
+frame = file.read_frame_position(2, 7)
+value = frame.get_value()
+print(f"frame {2, 7} -> {frame} {len(value)} bytes")
+```
 
-```shell
-dcm-getframe -o tile.raw data/test_files/sm_image.dcm 12
+This will print:
+
+```python
+$ ./read-frames.py sm_image.dcm
+opening libdicom ...
+init for libdicom ...
+libdicom version: 1.0.0
+frame 1 -> <10x10 pixels, 8 bits, 3 bands, RGB> 300 bytes
+frame 2 -> <10x10 pixels, 8 bits, 3 bands, RGB> 300 bytes
+frame 3 -> <10x10 pixels, 8 bits, 3 bands, RGB> 300 bytes
+...
 ```
 
-### From Python
+## Command-line tools
+
+libdicom comes with two small command-line tools which can be useful for
+testing.
 
-There's a sample Python binding here:
+`dcm-dump` will print all metadata from a DICOM file. It's fast, and can
+dump DICOM files of any size while using only a small amount of memory.
 
-https://github.com/ImagingDataCommons/pylibdicom
+For example:
 
-## Documentation
+```!
+$ dcm-dump sm_image.dcm
+===File Meta Information===
+(0002,0001) FileMetaInformationVersion | OB | 2 | 1 | 00 01
+(0002,0002) MediaStorageSOPClassUID | UI | 30 | 1 | 1.2.840.10008.5.1.4.1.1.77.1.6
+(0002,0003) MediaStorageSOPInstanceUID | UI | 64 | 1 | 1.2.826.0.1.3680043.9.7433.3.12857516184849951143044513877282227
+(0002,0010) TransferSyntaxUID | UI | 20 | 1 | 1.2.840.10008.1.2.1
+(0002,0012) ImplementationClassUID | UI | 28 | 1 | 1.2.826.0.1.3680043.9.7433.1
+(0002,0013) ImplementationVersionName | SH | 14 | 1 | wsiget v0.0.1
+...
+```
+
+`dcm-getframe` will read a single frame from a DICOM file.
+
+For example:
+
+```shell
+dcm-getframe -o tile.raw data/test_files/sm_image.dcm 12
+```
 
-User and developer guides as well as API documentation can be found at
-[libdicom.readthedocs.io](https://libdicom.readthedocs.io/en/latest/).
+To read frame 12.
 
-# Thanks
+## Thanks
 
 Development of this library was supported by [NCI Imaging Data
 Commons](https://imaging.datacommons.cancer.gov/), and has been funded in

meson.build

@@ -8,7 +8,7 @@ project(
   ],
   license : 'MIT',
   meson_version : '>=0.50',
-  version : '1.0.0-rc2'
+  version : '1.0.0'
 )
 if not meson.is_subproject()
   meson.add_dist_script(

src/dicom-dict.c

@@ -5134,7 +5134,7 @@ void dcm_init(void)
             struct _DcmAttribute_hash_entry *entry;
 
             // The "" keyword appears several times and is used for retired
-            // tags ... we can't map this to tags unambigiously, so we skip it
+            // tags ... we can't map this to tags unambiguously, so we skip it
             // in the table
             if (strcmp(attribute_table[i].keyword, "") == 0) {
                 continue;