openslide-vendor-mirax.c.patch

diff --git a/src/openslide-vendor-mirax.c b/src/openslide-vendor-mirax.c
index ffc03b3..4990416 100644
--- a/src/openslide-vendor-mirax.c
+++ b/src/openslide-vendor-mirax.c
@@ -32,6 +32,7 @@
 #include "openslide-decode-gdkpixbuf.h"
 #include "openslide-decode-jpeg.h"
 #include "openslide-decode-png.h"
+#include "openslide-decode-jp2k.h"
 
 #include <glib.h>
 #include <stdlib.h>
@@ -141,6 +142,7 @@ enum image_format {
   FORMAT_JPEG,
   FORMAT_PNG,
   FORMAT_BMP,
+  FORMAT_JPEG2000,
 };
 
 struct slide_zoom_level_section {
@@ -245,6 +247,24 @@ static uint32_t *read_image(openslide_t *osr,
                                        dest, w, h,
                                        err);
     break;
+  case FORMAT_JPEG2000: {
+      g_autofree void *buf = g_malloc(image->length);
+      int32_t buflen;
+      g_autoptr(_openslide_file) f = _openslide_fopen(data->datafile_paths[image->fileno], err);
+      if (!f) {
+        return false;
+      }
+      if (!_openslide_fseek(f, image->start_in_file, SEEK_SET, err)) {
+        g_prefix_error(err, "Couldn't fseek %s: ", data->datafile_paths[image->fileno]);
+        return false;
+      }
+      GError *tmp_err = NULL;
+      buflen = _openslide_fread(f, buf, image->length, &tmp_err);
+      result = _openslide_jp2k_decode_buffer(
+          dest, w, h,
+          buf, buflen, OPENSLIDE_JP2K_RGB, err);
+    }
+    break;
   default:
     g_assert_not_reached();
   }
@@ -397,6 +417,17 @@ static bool mirax_detect(const char *filename, struct _openslide_tifflike *tl,
     g_strndup(filename, strlen(filename) - strlen(MRXS_EXT));
   g_autofree char *slidedat_path =
     g_build_filename(dirname, SLIDEDAT_INI, NULL);
+  if (!_openslide_fexists(slidedat_path, &tmp_err)) {
+    g_autofree char *basename = g_path_get_dirname(filename);
+    if (basename) {
+      if (g_str_has_suffix(basename, MRXS_EXT)) {
+        g_free(slidedat_path);
+        g_free(dirname);
+        dirname = g_strndup(basename, strlen(basename) - strlen(MRXS_EXT));
+        slidedat_path = g_build_filename(dirname, SLIDEDAT_INI, SLIDEDAT_INI, NULL);
+      }
+    }
+  }
   if (!_openslide_fexists(slidedat_path, &tmp_err)) {
     if (tmp_err != NULL) {
       g_propagate_prefixed_error(err, tmp_err, "Testing whether %s exists: ",
@@ -973,6 +1004,8 @@ static enum image_format parse_image_format(const char *name, GError **err) {
     return FORMAT_PNG;
   } else if (!strcmp(name, "BMP24")) {
     return FORMAT_BMP;
+  } else if (!strcmp(name, "JPEG2000")) {
+    return FORMAT_JPEG2000;
   } else {
     g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
                 "Unrecognized image format: %s", name);
@@ -1359,8 +1392,10 @@ static int get_associated_image_nonhier_offset(GKeyFile *keyfile,
   // verify image format
   // we have only ever seen JPEG
   if (parse_image_format(format, NULL) != FORMAT_JPEG) {
+    /*
     g_set_error(err, OPENSLIDE_ERROR, OPENSLIDE_ERROR_FAILED,
                 "Unsupported associated image format: %s", format);
+    */
     return -1;
   }
 
@@ -1373,10 +1408,22 @@ static bool mirax_open(openslide_t *osr, const char *filename,
   // get directory from filename
   g_autofree char *dirname =
     g_strndup(filename, strlen(filename) - strlen(MRXS_EXT));
+  bool girder_paths = false;
+  GError *tmp_err = NULL;
+  g_autofree char *slidedat_path2 =
+    g_build_filename(dirname, SLIDEDAT_INI, NULL);
+  if (!_openslide_fexists(slidedat_path2, &tmp_err)) {
+    g_free(dirname);
+    g_autofree char *basename = g_path_get_dirname(filename);
+    dirname = g_strndup(basename, strlen(basename) - strlen(MRXS_EXT));
+    girder_paths = true;
+  }
 
   // first, check slidedat
   g_autofree char *slidedat_path =
-    g_build_filename(dirname, SLIDEDAT_INI, NULL);
+    !girder_paths ?
+    g_build_filename(dirname, SLIDEDAT_INI, NULL) :
+    g_build_filename(dirname, SLIDEDAT_INI, SLIDEDAT_INI, NULL);
   // hash the slidedat
   if (!_openslide_hash_file(quickhash1, slidedat_path, err)) {
     return false;
@@ -1409,7 +1456,7 @@ static bool mirax_open(openslide_t *osr, const char *filename,
   READ_KEY_OR_FAIL(objective_magnification, slidedat, GROUP_GENERAL,
                    KEY_OBJECTIVE_MAGNIFICATION, integer);
 
-  GError *tmp_err = NULL;
+  tmp_err = NULL;
   int image_divisions =
     g_key_file_get_integer(slidedat, GROUP_GENERAL,
                            KEY_CAMERA_IMAGE_DIVISIONS_PER_SIDE, &tmp_err);
@@ -1499,7 +1546,7 @@ static bool mirax_open(openslide_t *osr, const char *filename,
     g_autofree char *key = g_strdup_printf(KEY_d_FILE, i);
     g_autofree char *name = NULL;
     READ_KEY_OR_FAIL(name, slidedat, GROUP_DATAFILE, key, value);
-    datafile_paths[i] = g_build_filename(dirname, name, NULL);
+    datafile_paths[i] = !girder_paths ? g_build_filename(dirname, name, NULL) : g_build_filename(dirname, name, name, NULL);
   }
 
   // load data from all slide_zoom_level_section_names sections
@@ -1624,7 +1671,7 @@ static bool mirax_open(openslide_t *osr, const char *filename,
   */
 
   // read indexfile
-  g_autofree char *index_path = g_build_filename(dirname, index_filename, NULL);
+  g_autofree char *index_path = !girder_paths ? g_build_filename(dirname, index_filename, NULL) : g_build_filename(dirname, index_filename, index_filename, NULL);
   g_autoptr(_openslide_file) indexfile = _openslide_fopen(index_path, err);
   if (!indexfile) {
     return false;