Fix widget with Python 3.9. Fix flipY for lat-reversed data sets. Bum…

…p to 0.4.14.

README.md

@@ -29,7 +29,7 @@ Example notebooks can be found in the [examples](https://github.com/msoechting/l
 
 ## Attribution
 
-When using Lexcube in your research, please cite:
+When using Lexcube and/or generated images, please acknowledge/cite:
 ```bibtex
 @ARTICLE{soechting2024lexcube,
   author={Söchting, Maximilian and Mahecha, Miguel D. and Montero, David and Scheuermann, Gerik},
@@ -101,7 +101,7 @@ If you are using Jupyter within VSCode, you may have to add the following to you
         "unpkg.com"
     ],
 ```
-This allows the Lexcube JavaScript front-end files to be downloaded from these sources ([read more](https://github.com/microsoft/vscode-jupyter/wiki/IPyWidget-Support-in-VS-Code-Python)).
+If you are working on a remote server in VSCode, do not forget to set this setting also there! This allows the Lexcube JavaScript front-end files to be downloaded from these sources ([read more](https://github.com/microsoft/vscode-jupyter/wiki/IPyWidget-Support-in-VS-Code-Python)).
 
 ## Installation
 

examples/1_introduction.ipynb

@@ -40,7 +40,7 @@
    "outputs": [],
    "source": [
     "# ** Option 1: Use a numpy data set\n",
-    "# ds = np.sum(np.mgrid[0:256,0:256,0:256], axis=0)"
+    "# data_source = np.sum(np.mgrid[0:256,0:256,0:256], axis=0)"
    ]
   },
   {
@@ -50,7 +50,7 @@
    "outputs": [],
    "source": [
     "# ** Option 2: Load a local xarray data set\n",
-    "# ds = xr.open_dataset(\"/data/my_data_set.zarr\", chunks={}, engine=\"zarr\")"
+    "# data_source = xr.open_dataset(\"/data/my_data_set.zarr\", chunks={}, engine=\"zarr\")"
    ]
   },
   {

lexcube/_frontend.py

@@ -22,4 +22,4 @@
 """
 
 module_name = "lexcube"
-module_version = "^0.4.13"
+module_version = "^0.4.14"

lexcube/_version.py

@@ -17,4 +17,4 @@
 # You should have received a copy of the GNU General Public License
 # along with this program.  If not, see <https://www.gnu.org/licenses/>.
 
-__version__ = "0.4.13"
+__version__ = "0.4.14"

lexcube/cube3d.py

@@ -21,7 +21,10 @@
 import datetime
 import math
 import asyncio
-from traitlets import Unicode, Dict, Float, Union, List, Int, validate, TraitError, Bool, Tuple
+from traitlets import Unicode, Dict, Float, List, Int, validate, TraitError, Bool, Tuple
+import traitlets
+from typing import Union
+
 from ._frontend import module_name, module_version
 import ipywidgets as widgets
 from lexcube.lexcube_server.src.lexcube_widget import start_tile_server_in_widget_mode
@@ -56,7 +59,7 @@ class Cube3DWidget(widgets.DOMWidget):
     request_progress = Dict().tag(sync=True)
     vmin = Float(allow_none=True).tag(sync=True)
     vmax = Float(allow_none=True).tag(sync=True)
-    cmap = Union([Unicode(), List()], allow_none=True).tag(sync=True)
+    cmap = traitlets.Union([Unicode(), List()], allow_none=True).tag(sync=True)
     xlim = Tuple(Int(), Int(), default_value=(-1, -1)).tag(sync=True)
     ylim = Tuple(Int(), Int(), default_value=(-1, -1)).tag(sync=True)
     zlim = Tuple(Int(), Int(), default_value=(-1, -1)).tag(sync=True)
@@ -67,7 +70,7 @@ class Cube3DWidget(widgets.DOMWidget):
 
     isometric_mode = Bool(False).tag(sync=True)
 
-    def __init__(self, data_source, cmap: str | list | None = None, vmin: float | None = None, vmax: float | None = None, isometric_mode: bool = False, use_lexcube_chunk_caching: bool = True, **kwargs):
+    def __init__(self, data_source, cmap: Union[str, list, None] = None, vmin: Union[float, None] = None, vmax: Union[float, None] = None, isometric_mode: bool = False, use_lexcube_chunk_caching: bool = True, **kwargs):
         super().__init__(**kwargs)
         self.cmap = cmap
         self.vmin = vmin

lexcube/lexcube_server/requirements-core.txt

@@ -1,5 +1,7 @@
+s3fs==2023.12.2
 bottleneck==1.3.7
 cachey==0.2.1
+dask==2024.1.1
 netCDF4==1.6.5
 opencv-python-headless==4.8.1.78
 psutil==5.9.6

lexcube/lexcube_server/src/lexcube_widget.py

@@ -16,12 +16,13 @@
 
 from __future__ import annotations
 from .tile_server import TileServer, calculate_max_lod, API_VERSION, get_dimension_labels
+from typing import Union
 import ipywidgets as widgets
 import numpy as np
 import xarray as xr
 
 
-def start_tile_server_in_widget_mode(widget: widgets.DOMWidget, data_source: xr.DataArray | np.ndarray, use_lexcube_chunk_caching: bool):
+def start_tile_server_in_widget_mode(widget: widgets.DOMWidget, data_source: Union[xr.DataArray, np.ndarray], use_lexcube_chunk_caching: bool):
     if type(data_source) not in [xr.DataArray, np.ndarray]:
         print("Error: Input data is not xarray.DataArray or numpy.ndarray")
         raise Exception("Error: Input data is not xarray.DataArray or numpy.ndarray")

lexcube/lexcube_server/src/tile_server.py

@@ -42,6 +42,7 @@
 import xarray as xr
 import zfpy
 from dask.cache import Cache
+from typing import Union
 
 UNCOMPRESSED_SUFFIX = "_uncompressed"
 ANOMALY_PARAMETER_ID_SUFFIX = "_lxc_anomaly"
@@ -56,7 +57,7 @@
 TILE_FORMAT_MAGIC_BYTES = "lexc".encode("utf-8") # 6c 65 78 63, magic bytes to recognize lexcube tiles
 
 class DataSourceProxy:
-    def __init__(self, data_source: np.ndarray | xr.DataArray) -> None:
+    def __init__(self, data_source: Union[xr.DataArray, np.ndarray]) -> None:
         self.data_source = data_source
         self.cache_chunks = type(data_source) == xr.DataArray and data_source.chunks and len(data_source.chunks) > 0
         self.shape = self.data_source.shape
@@ -109,7 +110,7 @@ def get_chunk(self, iz: int, iy: int, ix: int):
             self.chunk_cache[chunk_key] = self.data_source[slices].values
         return self.chunk_cache[chunk_key]
 
-    def validate_slice(self, s: slice | int, dimension: int):
+    def validate_slice(self, s: Union[slice, int], dimension: int):
         if type(s) == int:
             s = slice(s, s + 1)
         return slice(max(s.start, 0), min(s.stop, self.shape[dimension]))
@@ -152,7 +153,7 @@ def compress_nan_mask(self, nan_mask: bytes) -> bytes:
     def decompress_nan_mask(self, data: bytes) -> bytes:
         return self.nan_mask_compressor.decode(data)
 
-    def get_tile_data_compressor(self, use_lossless_override: (None | bool) = None):
+    def get_tile_data_compressor(self, use_lossless_override: Union[bool, None] = None):
         lossless = self.compress_lossless if use_lossless_override == None else use_lossless_override
         if lossless:
             return self.tile_data_compressor_lossless
@@ -164,7 +165,7 @@ def compress_tile_data(self, tile_data: bytes, is_anomaly_tile: bool = False) ->
             self.tile_data_compressor_default.tolerance = self.anomaly_compression_tolerance if is_anomaly_tile else self.default_compression_tolerance
         return self.get_tile_data_compressor().encode(tile_data)
 
-    def decompress_tile_data(self, tile_data: bytes, use_lossless_override: (None | bool) = None) -> bytes:
+    def decompress_tile_data(self, tile_data: bytes, use_lossless_override: Union[bool, None] = None) -> bytes:
         return self.get_tile_data_compressor(use_lossless_override).decode(tile_data)
 
 
@@ -241,21 +242,20 @@ def patch_data(data: np.ndarray, dataset_id: str, parameter: str, dataset_config
     if parameter == "snow_water_equivalent":
         data = np.where(data==-1, np.nan, data) # -1 = Oceans = NaN
         data = np.where(data==-2, 0, data) # -2 = mountains or something...
-    if dataset_config and dataset_config.flipped_y:
-        data = np.flip(data, axis=1)
     return data
 
-def patch_dataset(ds: xr.DataArray | np.ndarray):
+def patch_dataset(ds: Union[xr.DataArray, xr.Dataset, np.ndarray]):
     if type(ds) == np.ndarray:
         return ds
     # Some datasets from xee (Google Earth Engine) have (time, lon, lat) dimension order, fix that here:
-    if ds.dims[1] in LONGITUDE_DIMENSION_NAMES and ds.dims[2] in LATITUDE_DIMENSION_NAMES:
-        ds = ds.transpose(ds.dims[0], ds.dims[2], ds.dims[1])
+    dims = list(ds.dims)
+    if dims[1] in LONGITUDE_DIMENSION_NAMES and dims[2] in LATITUDE_DIMENSION_NAMES:
+        ds = ds.transpose(dims[0], dims[2], dims[1])
     # For data sets where the latitude is sorted by descending values (turning the world upside down), flip that:
-    if ds.dims[1] in LATITUDE_DIMENSION_NAMES:
-        lat_values = ds[ds.dims[1]]
+    if dims[1] in LATITUDE_DIMENSION_NAMES:
+        lat_values = ds[dims[1]]
         if lat_values[0] < lat_values[len(lat_values) - 1]:
-            ds = np.flip(ds, axis=1)
+            ds = ds.sortby(dims[1], ascending=False)
     return ds
 
 def open_dataset(config: ServerConfig, path: str):
@@ -288,7 +288,6 @@ def __init__(self, dataset_config: dict) -> None:
         self.calculate_anomalies = bool(dataset_config.get("calculateYearlyAnomalies") or False)
         self.force_tile_generation = bool(dataset_config.get("forceTileGeneration") or False) 
         self.max_lod = int(dataset_config.get("overrideMaxLod") or -1) 
-        self.flipped_y = bool(dataset_config.get("flippedY") or False) 
         self.use_offline_metadata = bool(dataset_config.get("useOfflineMetadata") or False) 
         self.min_max_values_approximate_only = bool(dataset_config.get("approximateMinMaxValues") or True) 
 
@@ -382,9 +381,6 @@ def load_from_dataset(self, dataset: Dataset, data: xr.Dataset):
             "z": get_dimension_labels(data, self.z_dimension_name, self.z_dimension_type)
         }
 
-        if dataset.dataset_config.flipped_y:
-            self.axis_labels["y"] = self.axis_labels["y"][::-1]
-
 class ParameterMetadataParser:
     def __init__(self, config: ServerConfig, min_max_values_approximate_only: bool, dataset_path: str, dataset_id: str) -> None:
         self.min_max_values_approximate_only = min_max_values_approximate_only
@@ -557,7 +553,6 @@ def __init__(self, server_config: ServerConfig, dataset_config: dict, base_dir:
         self.x_max = -1
         self.y_max = -1
         self.z_max = -1
-        self.flipped_y = self.dataset_config.flipped_y
         self.tile_size = tile_size
         self.use_offline_metadata = self.dataset_config.use_offline_metadata
         self.meta_data = DatasetMetadata()
@@ -817,7 +812,7 @@ def get_anomaly_tile(self):
     def get_hash_key(self):
         return "-".join([self.dataset_id, self.parameter, str(self.index_dimension.value), str(self.index_value), str(self.lod), str(self.x), str(self.y)])
 
-    def generate_from_data(self, source_data: np.ndarray | xr.DataArray | DataSourceProxy, tile_compressor: TileCompressor, z_offset: int = 0, added_compression_error: float = 0.0, resample_resolution: int = 1, compress_lossless: bool = False):
+    def generate_from_data(self, source_data: Union[xr.DataArray, np.ndarray, DataSourceProxy], tile_compressor: TileCompressor, z_offset: int = 0, added_compression_error: float = 0.0, resample_resolution: int = 1, compress_lossless: bool = False):
         lod_factor = pow(2, self.lod)
         inverse_lod_factor = 1 / lod_factor
         lod_tile_size = lod_factor * self.tile_size
@@ -887,7 +882,7 @@ def write_to_intermediate_single_file(self, path: str, compressed_data: bytes, s
     def get_tile_metadata_bytes(self, resample_resolution: int, nan_mask_length: int, max_error_or_magic_number: float):
         return TILE_FORMAT_MAGIC_BYTES + struct.pack("<I", TILE_VERSION) + struct.pack("<I", resample_resolution) + struct.pack("<I", nan_mask_length) + struct.pack("<d", max_error_or_magic_number)        
 
-    def compress_data(self, source_values: np.ndarray | xr.DataArray, tile_compressor: TileCompressor, resample_resolution: int = 1, added_compression_error: float = 0.0):
+    def compress_data(self, source_values: Union[xr.DataArray, np.ndarray], tile_compressor: TileCompressor, resample_resolution: int = 1, added_compression_error: float = 0.0):
         if np.all(np.isnan(source_values)):
             return self.get_tile_metadata_bytes(0, 0, NAN_TILE_MAGIC_NUMBER)
         # if np.any(np.isnan(source_values)):
@@ -1027,7 +1022,7 @@ def update_progress(self, request_group_id: int, request_id: int, done: int, tot
             total = sum(c[1] for c in current.values())
             self.widget_update_progress([done, total])
 
-    def startup_widget(self, data_source: xr.DataArray | np.ndarray, use_lexcube_chunk_caching: bool):
+    def startup_widget(self, data_source: Union[xr.DataArray, np.ndarray], use_lexcube_chunk_caching: bool):
         if type(data_source) == xr.DataArray and not data_source.chunks:
             print("Xarray input object does not have chunks. You can re-open with 'chunks={}' to enable dask for caching and progress reporting functionality - but may be overall slower for small data sets.")
         dask_cache = Cache(2e9)  # Leverage two gigabytes of memory

package.json

@@ -1,6 +1,6 @@
 {
   "name": "lexcube",
-  "version": "0.4.13",
+  "version": "0.4.14",
   "description": "Lexcube: 3D Data Cube Visualization in Jupyter Notebooks",
   "keywords": [
     "jupyter",

pyproject.toml

@@ -45,7 +45,7 @@ dependencies = [
     "zarr>=2.14.2",
     "zfpy>=1.0.0",
 ]
-version = "0.4.13"
+version = "0.4.14"
 
 [project.optional-dependencies]
 docs = [
@@ -109,7 +109,7 @@ build_cmd = "build:prod"
 github_url = "https://github.com/msoechting/lexcube/"
 
 [tool.tbump.version]
-current = "0.4.13"
+current = "0.4.14"
 
 # Example of a semver regexp.
 # Make sure this matches current_version before

src/lexcube-client/src/client/client.ts

@@ -129,9 +129,10 @@ class CubeClientContext {
     }
 
     async startup() {
+        this.networking.connect();
         await this.interaction.startup();
         this.rendering.startup();
-        await this.networking.connect();
+        this.networking.postStartup();
         this.postStartup();
     }
 

src/lexcube-client/src/client/constants.ts

@@ -78,6 +78,6 @@ const DEFAULT_WIDGET_HEIGHT = 768;
 const API_VERSION = 5;
 const TILE_VERSION = 2;
 
-const PACKAGE_VERSION = "0.4.13";
+const PACKAGE_VERSION = "0.4.14";
 
 export { DeviceOrientation, PACKAGE_VERSION, positiveModulo, range, getIndexDimensionOfFace, getAddressedFacesOfDimension, getFacesOfIndexDimension, capitalizeString, DEFAULT_WIDGET_WIDTH, DEFAULT_WIDGET_HEIGHT, DEFAULT_COLORMAP, ANOMALY_PARAMETER_ID_SUFFIX, TILE_FORMAT_MAGIC_BYTES, TILE_VERSION, TILE_SIZE, MAX_ZOOM_FACTOR, NAN_TILE_MAGIC_NUMBER, LOSSLESS_TILE_MAGIC_NUMBER, NAN_REPLACEMENT_VALUE, COLORMAP_STEPS, NOT_LOADED_REPLACEMENT_VALUE, API_VERSION, Dimension, CubeFace }

src/lexcube-client/src/client/index.html

@@ -79,6 +79,17 @@
         </div>
     </div>
 
+    <div class="fullscreen-wrapper nopointer noselect" style="top: 15px; left: 15px;">
+        <img src="lexcube-logo.png" style="width: calc(max(300px, 17vw)); opacity: 0.9;"/>
+    </div>
+
+    <div class="noselect top-left-ui ui-normal jupyter-notification" onclick="this.style.display = 'none';localStorage.setItem('dismiss-jupyter', `${Date.now()}`);" style="padding: 1px;">
+        <a href='https://github.com/msoechting/lexcube' target='_blank'><div style="background-image: url('lexcube-jupyter.png'); width: 337px;;
+        height: 140px;background-size: contain; cursor:pointer"></div></a>
+        <div class="close-button" onclick="this.parentNode.onclick()"></div>
+    </div>
+<!-- <a href="https://github.com/msoechting/lexcube" target="_blank" style="width: 100%; height: 100%;"></a> -->
+
     <div class="ui-normal noselect options-ui" style="display: none;">
         <button type="button" class="collapsible-button" onclick="this.parentNode.style.display = 'none';">Close</button>
         <hr>
@@ -151,12 +162,12 @@ <h3 class="noselect expert-mode" style="cursor: pointer;" onclick="let g = this.
         <div class="ui-normal flex-col-center dataset-info-window">
             <div class="dataset-info" style="max-width: 100%; overflow-y: auto; overflow-x: hidden;"></div>
 
-            <div style="width: 100%; text-align: center;">  
+            <div style="width: 100%; text-align: center;"> 
                 <hr>
                 <div class="expert-mode">
                     LexCube is an interactive visualization of large-scale earth data sets. Created at Leipzig University by Maximilian Söchting.
                 </div>
-                <p xmlns:cc="http://creativecommons.org/ns#" xmlns:dct="http://purl.org/dc/terms/">Images generated by <a property="dct:title" rel="cc:attributionURL" target="_blank" href="https://www.lexcube.org">LexCube - Leipzig Explorer of Earth Data Cubes</a> by <a rel="cc:attributionURL dct:creator" property="cc:attributionName" target="_blank" href="https://rsc4earth.de/authors/msoechting/">Maximilian Söchting</a> are licensed under <a href="http://creativecommons.org/licenses/by/4.0/?ref=chooser-v1" target="_blank" rel="license noopener noreferrer" style="display:inline-block;">CC BY 4.0<img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/cc.svg?ref=chooser-v1"><img style="height:22px!important;margin-left:3px;vertical-align:text-bottom;" src="https://mirrors.creativecommons.org/presskit/icons/by.svg?ref=chooser-v1"></a></p> 
+                <div><b>When using Lexcube and generated images acknowledge/cite</b>: M. Söchting, M. D. Mahecha, D. Montero and G. Scheuermann, "Lexcube: Interactive Visualization of Large Earth System Data Cubes," in IEEE Computer Graphics and Applications, vol. 44, no. 1, pp. 25-37, Jan.-Feb. 2024, doi: <a href="https://www.doi.org/10.1109/MCG.2023.3321989" target="_blank">10.1109/MCG.2023.3321989</a>.</div>
 
                 <div class="expert-mode">
                     Client Version: <%= htmlWebpackPlugin.options.version %> (Commit: <%= htmlWebpackPlugin.options.commitDate %>, Build: <%= htmlWebpackPlugin.options.buildDate %>)
@@ -254,6 +265,15 @@ <h1>Craft Your Data Cube!</h1>
         const b = document.body;
         if (document.URL.indexOf("localhost") != -1) {
             b.getElementsByClassName("tutorial-wrapper")[0].style.display = "none";
+            try {
+                const c = localStorage.getItem('dismiss-jupyter');
+                const v = parseInt(c);
+                const notificationInterval = 1000 * 60 * 60 * 24 * 2; // 2 days
+                if (!isNaN(v) && Date.now() - v < notificationInterval) {
+                    b.getElementsByClassName("jupyter-notification")[0].style.display = "none";
+                }
+            } catch (e) {
+            }
         }
         var touchDevice = ('ontouchstart' in window) || (navigator.maxTouchPoints > 0);
         b.getElementsByClassName("tutorial-mouse")[0].style.display = touchDevice ? 'none' : 'block';