Merge branch 'TissUUmaps:master' into master

Author: cavenel

CHANGELOG.md

@@ -1,5 +1,24 @@
 # Changelog
 
+## 3.2.1
+
+- Add scalebar to capture
+- Add project tab with project settings
+
+## 3.2.0.5
+
+- Fix MacOs X libvips issue with 90% jpeg compression
+- Make top menu collapsible in config
+- Add project list and description in upper corner (optional)
+
+## 3.2.0.4
+
+- Run Docker container as non-root user
+- Allow marker size slider to be used with absolute scaling
+- Fix incorrect transforms of region points when image layer is flipped
+- Fix MacOS X libvps issue with percent value
+- Add new blend modes for marker rendering
+
 ## 3.2
 
 - Add annotation tools (in collaboration with Sanofi Digital R&D)

container/Dockerfile

@@ -1,5 +1,11 @@
 FROM python:3.10-alpine
 
+# Set usertmap as a variable
+ENV USER=usertmap
+
+# Create a non-root user
+RUN adduser -D $USER
+
 COPY ./container/requirements.txt /requirements.txt
 
 # Install libvips
@@ -41,11 +47,14 @@ RUN pip3 install gunicorn gevent
 
 COPY ./container/tissuumaps.cfg /tissuumaps.cfg
 COPY ./tissuumaps/ /app/tissuumaps
+
+# Set up permissions and environment variables
 WORKDIR /app/
 ENV PYTHONPATH /app
-
 ENV GUNICORN_CMD_ARGS "--bind=0.0.0.0:80 --workers=8 --thread=8 --worker-class=gevent --forwarded-allow-ips='*' -"
-
 ENV TISSUUMAPS_CONF /tissuumaps.cfg
 
+# Change to the non-root user
+USER $USER
+
 CMD ["gunicorn", "tissuumaps:app"]

container/requirements.txt

@@ -7,4 +7,4 @@ pyvips>=2.1.14
 matplotlib>=3.2.2
 pyyaml>=6.0
 h5py>=3.6.0
-tissuumaps-schema~=1.2.0
+tissuumaps-schema~=1.3.0

plugins_repo/3.1/DEPICTER.gif

@@ -3,5 +3,5 @@ name: DEPICTER
 version: 0.1.0
 author: Eduard Chelebian - Christophe Avenel
 date: 2023-08-08
-image:
+image: DEPICTER.gif
 description:

plugins_repo/latest/DEPICTER.gif

@@ -22,6 +22,11 @@ InteractionQC = {
       type: "section",
       collapsed: true,
     },
+    _uns_postfix: {
+      label: "For HDF5 files, postfix of the uns key containing the matrix:",
+      type: "text",
+      default: "/uns/{obs}_nhood_enrichment/zscore",
+    },
   },
   _matrix: null,
   _matrix_header: null,
@@ -53,7 +58,7 @@ InteractionQC.init = function (container) {
     kind: "label",
     extraAttributes: { for: "matrix" },
   });
-  label412.innerText = "Select file";
+  label412.innerText = "For CSV file, select it on disk:";
 
   input411.addEventListener("change", (event) => {
     var reader = new FileReader();
@@ -136,12 +141,16 @@ InteractionQC.loadFromH5AD = async function () {
   data_obj = dataUtils.data[_dataset];
   if (!data_obj._filetype == "h5") return;
   try {
-    let obs = data_obj._gb_col.replace(/\/obs/g, "");
+    let obs = data_obj._gb_col.replace(/\/obs/g, "").replace(/\//g, "");
+    InteractionQC._className = obs;
     let matrix = await dataUtils._hdf5Api.get(data_obj._csv_path, {
-      path: "/uns/" + obs + "_nhood_enrichment/zscore",
+      path: InteractionQC.get("_uns_postfix").replace("{obs}", obs),
     });
     console.log(matrix);
-    let _matrix_header = Object.keys(data_obj._groupgarden);
+    let _matrix_header = await dataUtils._hdf5Api.get(data_obj._csv_path, {
+      path: "/obs/" + obs + "/categories",
+    });
+    _matrix_header = _matrix_header.value;
     // convert matrix from 1D typed array of shape NxN to array of arrays
 
     InteractionQC._matrix = [];
@@ -173,6 +182,8 @@ InteractionQC.run = async function () {
   let _matrix_header = InteractionQC._matrix_header;
   if (!InteractionQC._matrix_header) {
     _matrix_header = await InteractionQC.loadFromH5AD();
+  } else {
+    InteractionQC._className = "Cell classes";
   }
   var op = tmapp["object_prefix"];
 
@@ -197,18 +208,19 @@ InteractionQC.run = async function () {
       tickvals: _matrix_header,
       ticktext: _matrix_header.map(function (text) {
         let color = document.getElementById(
-          _dataset + "_" + text + "_color",
+          _dataset + "_" + text.replace(/ /g, "_") + "_color",
         )?.value;
-        return "<span style='font-weight:bold;color:" + color + "'>███</span>";
+        return "<span style='font-weight:bold;color:" + color + "'>█</span>";
       }),
       ticks: "",
-      tickangle: 90,
+      tickangle: 0,
       title: {
-        text: "Cell class 2",
+        text: InteractionQC._className,
         font: {
-          size: 25,
+          size: 20,
           color: "black",
         },
+        standoff: 20,
       },
     },
     xaxis: {
@@ -219,20 +231,19 @@ InteractionQC.run = async function () {
         .reverse()
         .map(function (text) {
           let color = document.getElementById(
-            _dataset + "_" + text + "_color",
+            _dataset + "_" + text.replace(/ /g, "_") + "_color",
           )?.value;
-          return (
-            "<span style='font-weight:bold;color:" + color + "'>███</span>"
-          );
+          return "<span style='font-weight:bold;color:" + color + "'>█</span>";
         }),
       ticks: "",
-      tickangle: 0,
+      tickangle: 90,
       title: {
-        text: "Cell class 1",
+        text: InteractionQC._className,
         font: {
-          size: 25,
+          size: 20,
           color: "black",
         },
+        standoff: 5,
       },
       ticklabelposition: "top",
       side: "top",
@@ -254,7 +265,7 @@ InteractionQC.run = async function () {
   let legend = "";
   for (type of _matrix_header) {
     let typecolor = document.getElementById(
-      _dataset + "_" + type + "_color",
+      _dataset + "_" + type.replace(/ /g, "_") + "_color",
     )?.value;
     legend +=
       "<div style='display:inline-block;margin-right:10px;'><span style='width:15px;color:" +
@@ -285,6 +296,13 @@ InteractionQC.run = async function () {
               data.points[i].y.toPrecision(4) + '\n\n';
       }
       alert('Closest point clicked:\n\n'+pts);*/
+    })
+    .on("plotly_doubleclick", function () {
+      setTimeout(function () {
+        var uid = _dataset;
+        document.getElementById(uid + "_all_check").checked = false;
+        document.getElementById(uid + "_all_check").click();
+      }, 200);
     });
 };
 

plugins_repo/latest/DEPICTER.yml

@@ -1,6 +1,6 @@
 ---
 name: InteractionV&QC plugin
-version: 1.1
+version: 1.1.2
 author: Andrea Behanova, Christophe Avenel
 date: 2022-10-31
 image: InteractionQC.gif

plugins_repo/latest/InteractionQC.js

@@ -31,7 +31,7 @@ install_requires =
     h5py>=3.6.0
     scipy>=1.10.1
     packaging>=21.0
-    tissuumaps-schema~=1.2.0
+    tissuumaps-schema~=1.3.0
 
 [options.entry_points]
 console_scripts =

plugins_repo/latest/InteractionQC.yml

@@ -9,4 +9,4 @@ matplotlib>=3.2.2
 pyyaml>=5.0
 h5py>=3.6.0
 scipy>=1.10.1
-tissuumaps-schema~=1.2.0
+tissuumaps-schema~=1.3.0

setup.cfg

@@ -1 +1 @@
-3.2.0.1
+3.2.1.4

standalone/requirements.txt

@@ -30,16 +30,24 @@
 SLIDE_DIR = "/mnt/data/shared/"
 DEFAULT_PROJECT = False
 SLIDE_CACHE_SIZE = 60
+
 DEEPZOOM_FORMAT = "jpeg"
 DEEPZOOM_TILE_SIZE = 254
 DEEPZOOM_OVERLAP = 1
 DEEPZOOM_LIMIT_BOUNDS = True
 DEEPZOOM_TILE_QUALITY = 90
 
-FOLDER_DEPTH = 4
-PLUGINS = []
+VIPS_MIN_OUTLIER_PERC = 0.5
+VIPS_MAX_OUTLIER_PERC = 99.5
+VIPS_FORCE_RESCALE = False
+VIPS_JPEG_COMPRESSION = 85
+VIPS_EXCLUDE_MIN_INTENSITY = False
 
+PLUGINS = []
+DEBUG_CLI = False
 READ_ONLY = False
+COLLAPSE_TOP_MENU = False
+PROJECT_LIST = False
 
 # determine if application is a script file or frozen exe
 if getattr(sys, "frozen", False):
@@ -69,6 +77,10 @@
     os.path.expanduser("~"), ".tissuumaps", "plugins"
 )
 app.config.from_envvar("TISSUUMAPS_CONF", silent=True)
+userConfigFile = os.path.join(os.path.expanduser("~"), ".tissuumaps", "tissuumaps.cfg")
+
+if os.path.isfile(userConfigFile):
+    app.config.from_pyfile(userConfigFile)
 
 
 def getPluginInFolder(folder):

tissuumaps/VERSION

@@ -75,14 +75,6 @@ def main():
         type="int",
         help="tile size [254]",
     )
-    parser.add_option(
-        "-D",
-        "--depth",
-        metavar="LEVELS",
-        dest="FOLDER_DEPTH",
-        type="int",
-        help="folder depth search for opening files [4]",
-    )
     parser.add_option(
         "-r",
         "--readonly",

tissuumaps/__init__.py

@@ -967,6 +967,7 @@ def main():
 
     if opts.DEBUG:
         views.app.config["DEBUG_CLI"] = True
+    if views.app.config["DEBUG_CLI"]:
         log = logging.getLogger("werkzeug")
         log.setLevel(logging.DEBUG)
         log = logging.getLogger("pyvips")
@@ -982,7 +983,6 @@ def main():
 
         # os.environ['WERKZEUG_RUN_MAIN'] = 'true'
     else:
-        views.app.config["DEBUG_CLI"] = False
         log = logging.getLogger("werkzeug")
         log.setLevel(logging.ERROR)
         log = logging.getLogger("pyvips")

tissuumaps/__main__.py

@@ -150,7 +150,13 @@ def h5ad_to_tmap(basedir, path, library_id=None):
         "tSNE",
     ]:
         if coordinates in list(adata.get("obsm", [])):
-            globalX, globalY = f"/obsm/{coordinates};0", f"/obsm/{coordinates};1"
+            if (
+                isinstance(adata.get(f"/obsm/{coordinates}"), h5py.Group)
+                and "x" in adata.get(f"/obsm/{coordinates}").keys()
+            ):
+                globalX, globalY = f"/obsm/{coordinates}/x", f"/obsm/{coordinates}/y"
+            else:
+                globalX, globalY = f"/obsm/{coordinates};0", f"/obsm/{coordinates};1"
             break
 
     if list(adata.get("/obs/__categories/", [])) != []:
@@ -170,13 +176,6 @@ def h5ad_to_tmap(basedir, path, library_id=None):
 
     layers = []
     library_ids = list(adata.get("uns/spatial", []))
-    try:
-        library_ids = adata["/obs/library_id/categories"].asstr()[...]
-    except Exception:
-        try:
-            library_ids = adata["/obs/__categories/library_id"].asstr()[...]
-        except Exception:
-            pass
 
     coord_factor = 1
     for library_id in library_ids:
@@ -216,16 +215,28 @@ def h5ad_to_tmap(basedir, path, library_id=None):
             img = None
             import traceback
 
+            logging.error(traceback.format_exc())
+    try:
+        library_ids = adata["/obs/library_id/categories"][...]
+    except Exception:
+        import traceback
+
+        logging.error(traceback.format_exc())
+        try:
+            library_ids = adata["/obs/__categories/library_id"][...]
+        except Exception:
+            import traceback
+
             logging.error(traceback.format_exc())
 
     use_libraries = len(library_ids) > 1
 
     library_col = ""
     if use_libraries:
-        if "/obsm/spatial;" in globalX:
+        if "/obsm/spatial;" in globalX or "/obsm/X_spatial;" in globalX:
             try:
                 library_codes_array = adata["/obs/library_id/codes"][...]
-                library_categ_array = adata["/obs/library_id/categories"].asstr()[...]
+                library_categ_array = adata["/obs/library_id/categories"][...]
                 library_col = "/obs/library_id/codes"
             except Exception:
                 library_codes_array = adata["/obs/library_id"][...]
@@ -236,16 +247,21 @@ def h5ad_to_tmap(basedir, path, library_id=None):
                 if not write_adata:
                     write_adata = True
                     adata, path = get_write_adata(adata, path, basedir)
-                spatial_array = adata["/obsm/spatial"][()]
+                spatial_array = adata[globalX.split(";")[0]][()]
 
                 spatial_scaled_array = np.ones(spatial_array.shape)
                 for library_index, library_id in enumerate(library_categ_array):
-                    scale_factor = float(
-                        adata.get(
-                            f"/uns/spatial/{library_id}/scalefactors/tissue_{img_key}_scalef",
-                            1,
-                        )[()]
-                    )
+                    try:
+                        # Try to get the value from the specified path
+                        scale_factor = float(
+                            adata[
+                                f"/uns/spatial/{library_id}/scalefactors/tissue_{img_key}_scalef"
+                            ][()]
+                        )
+                    except (KeyError, TypeError, ValueError):
+                        # Set default value to 1 if
+                        # path does not exist or if there's an error
+                        scale_factor = 1.0
                     spatial_scaled_array[library_codes_array == library_index] = (
                         spatial_array[library_codes_array == library_index]
                         * scale_factor
@@ -292,14 +308,16 @@ def h5ad_to_tmap(basedir, path, library_id=None):
     obsListCategorical = []
     obsListNumerical = []
     palette = {}
-
-    obsIndex = str(adata.get("/obs").attrs["_index"])
+    try:
+        obsIndex = str(adata.get("/obs").attrs["_index"])
+    except Exception:
+        obsIndex = ""
     for obs in obsList:
         if adata.get(f"/obs/{obs}/categories") is not None:
             obsListCategorical.append(obs)
             p = getPalette(adata, obs)
             palette[obs] = p
-        elif adata.get(f"/obs/{obs}").dtype.kind in "iuf":
+        elif adata.get(f"/obs/{obs}") and adata.get(f"/obs/{obs}").dtype.kind in "iuf":
             obsListNumerical.append(obs)
         elif obs == obsIndex:
             continue