vitessce 3.7.7__py3-none-any.whl → 3.7.9__py3-none-any.whl

vitessce/data_utils/__init__.py

@@ -17,3 +17,14 @@ from .ome import (
 from .multivec import (
     adata_to_multivec_zarr,
 )
+from .spatialdata_points_zorder import (
+    # Function for computing codes and sorting
+    sdata_morton_sort_points,
+    # Other helper functions
+    sdata_points_process_columns,
+    sdata_points_write_bounding_box_attrs,
+    sdata_points_modify_row_group_size,
+    # Functions for querying
+    sdata_morton_query_rect,
+    row_ranges_to_row_indices,
+)

vitessce/data_utils/spatialdata_points_zorder.py

@@ -0,0 +1,514 @@
+from typing import Tuple, List, Optional
+
+import os
+from os.path import join
+from bisect import bisect_left, bisect_right
+import pandas as pd
+import numpy as np
+
+
+from spatialdata import get_element_annotators
+import dask.dataframe as dd
+import zarr
+
+
+MORTON_CODE_NUM_BITS = 32  # Resulting morton codes will be stored as uint32.
+MORTON_CODE_VALUE_MIN = 0
+MORTON_CODE_VALUE_MAX = 2**(MORTON_CODE_NUM_BITS / 2) - 1
+
+# --------------------------
+# Functions for computing Morton codes for SpatialData points (2D).
+# --------------------------
+
+
+def norm_series_to_uint(series, v_min, v_max):
+    """
+    Scale numeric Series (int or float) to integer grid [0, 2^bits-1], handling NaNs.
+    """
+    # Cast to float64
+    series_f64 = series.astype("float64")
+    # Normalize the array values to be between 0.0 and 1.0
+    norm_series_f64 = (series_f64 - v_min) / (v_max - v_min)
+    # Clip to ensure no values are outside 0/1 range
+    clipped_norm_series_f64 = np.clip(norm_series_f64, 0.0, 1.0)
+    # Multiply by the morton code max-value to scale from [0,1] to [0,65535]
+    out = (clipped_norm_series_f64 * MORTON_CODE_VALUE_MAX).astype(np.uint32)
+    # Set NaNs to 0.
+    out = out.fillna(0)
+    return out
+
+
+def norm_ddf_to_uint(ddf):
+    [x_min, x_max, y_min, y_max] = [ddf["x"].min().compute(), ddf["x"].max().compute(), ddf["y"].min().compute(), ddf["y"].max().compute()]
+    ddf["x_uint"] = norm_series_to_uint(ddf["x"], x_min, x_max)
+    ddf["y_uint"] = norm_series_to_uint(ddf["y"], y_min, y_max)
+
+    # Insert the bounding box as metadata for the sdata.points[element] Points element dataframe.
+    # TODO: does anything special need to be done to ensure this is saved to disk?
+    ddf.attrs["bounding_box"] = {
+        "x_min": float(x_min),
+        "x_max": float(x_max),
+        "y_min": float(y_min),
+        "y_max": float(y_max),
+    }
+
+    return ddf
+
+
+def _part1by1_16(x):
+    """
+    Spread each 16-bit value into 32 bits by inserting zeros between bits.
+    Input:  uint32 array (values must fit in 16 bits)
+    Output: uint32 array (bit-spread)
+    """
+
+    assert x.dtype.name == 'uint32'
+
+    # Mask away any bits above 16 (just in case input wasn't clean).
+    x = x & np.uint32(0x0000FFFF)
+
+    # First spread: shift left by 8 bits, OR with original, then mask.
+    # After this, groups of 8 bits are separated by 8 zeros.
+    x = (x | np.left_shift(x, 8)) & np.uint32(0x00FF00FF)
+
+    # Spread further: now groups of 4 bits separated by 4 zeros.
+    x = (x | np.left_shift(x, 4)) & np.uint32(0x0F0F0F0F)
+
+    # Spread further: groups of 2 bits separated by 2 zeros.
+    x = (x | np.left_shift(x, 2)) & np.uint32(0x33333333)
+
+    # Final spread: single bits separated by a zero bit.
+    # Now each original bit is in every other position (positions 0,2,4,...).
+    x = (x | np.left_shift(x, 1)) & np.uint32(0x55555555)
+
+    return x
+
+
+def _part1by1_32(x):
+    """
+    Spread each 32-bit value into 64 bits by inserting zeros between bits.
+    Input:  uint64 array (values must fit in 32 bits)
+    Output: uint64 array (bit-spread)
+    """
+
+    assert x.dtype.name == 'uint64'
+
+    # Mask away any bits above 32 (safety).
+    x = x.astype(np.uint64) & np.uint64(0x00000000FFFFFFFF)
+
+    # First spread: separate into 16-bit chunks spaced out.
+    x = (x | np.left_shift(x, 16)) & np.uint64(0x0000FFFF0000FFFF)
+
+    # Spread further: each 8-bit chunk separated.
+    x = (x | np.left_shift(x, 8)) & np.uint64(0x00FF00FF00FF00FF)
+
+    # Spread further: each 4-bit nibble separated.
+    x = (x | np.left_shift(x, 4)) & np.uint64(0x0F0F0F0F0F0F0F0F)
+
+    # Spread further: 2-bit groups separated.
+    x = (x | np.left_shift(x, 2)) & np.uint64(0x3333333333333333)
+
+    # Final spread: single bits separated by zeros.
+    # Now each original bit occupies every other position (0,2,4,...).
+    x = (x | np.left_shift(x, 1)) & np.uint64(0x5555555555555555)
+
+    return x
+
+
+def morton_interleave(ddf):
+    """
+    Vectorized Morton interleave for integer arrays xi, yi
+    already scaled to [0, 2^bits - 1].
+    Returns Morton codes as uint32 (if bits<=16) or uint64 (if bits<=32).
+    """
+
+    xi = ddf["x_uint"]
+    yi = ddf["y_uint"]
+
+    # Spread x and y bits into even (x) and odd (y) positions.
+    xs = _part1by1_16(xi)
+    ys = _part1by1_16(yi)
+
+    # Interleave: shift y bits left by 1 so they go into odd positions,
+    # then OR with x bits in even positions.
+    code = np.left_shift(ys.astype(np.uint64), 1) | xs.astype(np.uint64)
+
+    # Fits in 32 bits since we only had 16+16 input bits.
+    return code.astype(np.uint32)
+
+
+def sdata_morton_sort_points(sdata, element):
+    ddf = sdata.points[element]
+
+    # Compute morton codes
+    ddf = norm_ddf_to_uint(ddf)
+    ddf["morton_code_2d"] = morton_interleave(ddf)
+
+    if "z" in ddf.columns:
+        num_unique_z = ddf["z"].unique().shape[0].compute()
+        if num_unique_z < 100:
+            # Heuristic for interpreting the 3D data as 2.5D
+            # Reference: https://github.com/scverse/spatialdata/issues/961
+            sorted_ddf = ddf.sort_values(by=["z", "morton_code_2d"], ascending=True)
+        else:
+            # TODO: include z as a dimension in the morton code in the 3D case?
+
+            # For now, just return the data sorted by 2D code.
+            sorted_ddf = ddf.sort_values(by="morton_code_2d", ascending=True)
+    else:
+        sorted_ddf = ddf.sort_values(by="morton_code_2d", ascending=True)
+    sdata.points[element] = sorted_ddf
+
+    # annotating_tables = get_element_annotators(sdata, element)
+
+    # TODO: Sort any annotating table(s) as well.
+
+    return sdata
+
+
+def sdata_morton_query_rect_aux(sdata, element, orig_rect):
+    # orig_rect = [[50, 50], [100, 150]] # [[x0, y0], [x1, y1]]
+    # norm_rect = [
+    #    orig_coord_to_norm_coord(orig_rect[0], orig_x_min=0, orig_x_max=100, orig_y_min=0, orig_y_max=200),
+    #    orig_coord_to_norm_coord(orig_rect[1], orig_x_min=0, orig_x_max=100, orig_y_min=0, orig_y_max=200)
+    # ]
+
+    sorted_ddf = sdata.points[element]
+
+    # TODO: fail if no morton_code_2d column
+    # TODO: fail if not sorted as expected
+    # TODO: fail if no bounding box metadata
+
+    bounding_box = sorted_ddf.attrs["bounding_box"]
+    x_min = bounding_box["x_min"]
+    x_max = bounding_box["x_max"]
+    y_min = bounding_box["y_min"]
+    y_max = bounding_box["y_max"]
+
+    norm_rect = [
+        orig_coord_to_norm_coord(orig_rect[0], orig_x_min=x_min, orig_x_max=x_max, orig_y_min=y_min, orig_y_max=y_max),
+        orig_coord_to_norm_coord(orig_rect[1], orig_x_min=x_min, orig_x_max=x_max, orig_y_min=y_min, orig_y_max=y_max)
+    ]
+
+    # Get a list of morton code intervals that cover this rectangle region
+    # [ (morton_start, morton_end), ... ]
+    morton_intervals = zcover_rectangle(
+        rx0=norm_rect[0][0], ry0=norm_rect[0][1],
+        rx1=norm_rect[1][0], ry1=norm_rect[1][1],
+        bits=16,
+        stop_level=None,
+        merge=True,
+    )
+
+    return morton_intervals
+
+
+def sdata_morton_query_rect(sdata, element, orig_rect):
+    sorted_ddf = sdata.points[element]
+
+    # TODO: generalize to 3D morton codes
+
+    morton_intervals = sdata_morton_query_rect_aux(sdata, element, orig_rect)
+
+    # Get morton code column as a list of integers
+    morton_sorted = sorted_ddf["morton_code_2d"].compute().values.tolist()
+
+    # Get a list of row ranges that match the morton intervals.
+    # (This uses binary searches internally to find the matching row indices).
+    # [ (row_start, row_end), ... ]
+    matching_row_ranges = zquery_rows(morton_sorted, morton_intervals, merge=True)
+
+    return matching_row_ranges
+
+
+def sdata_morton_query_rect_debug(sdata, element, orig_rect):
+    # This is the same as the above sdata_morton_query_rect function,
+    # but it also returns the list of row indices that were checked
+    # during the binary searches.
+    sorted_ddf = sdata.points[element]
+    morton_intervals = sdata_morton_query_rect_aux(sdata, element, orig_rect)
+    morton_sorted = sorted_ddf["morton_code_2d"].compute().values.tolist()
+    matching_row_ranges, rows_checked = zquery_rows_aux(morton_sorted, morton_intervals, merge=True)
+    return matching_row_ranges, rows_checked
+
+# --------------------------
+# Functions for rectangle queries.
+# --------------------------
+
+# Convert a coordinate from the normalized [0, 65535] space to the original space.
+
+
+def norm_coord_to_orig_coord(norm_coord, orig_x_min, orig_x_max, orig_y_min, orig_y_max):
+    [norm_x, norm_y] = norm_coord
+    orig_x_range = orig_x_max - orig_x_min
+    orig_y_range = orig_y_max - orig_y_min
+    return [
+        (orig_x_min + (norm_x / MORTON_CODE_VALUE_MAX) * orig_x_range),
+        (orig_y_min + (norm_y / MORTON_CODE_VALUE_MAX) * orig_y_range),
+    ]
+
+# Convert a coordinate from the original space to the [0, 65535] normalized space.
+
+
+def orig_coord_to_norm_coord(orig_coord, orig_x_min, orig_x_max, orig_y_min, orig_y_max):
+    [orig_x, orig_y] = orig_coord
+    orig_x_range = orig_x_max - orig_x_min
+    orig_y_range = orig_y_max - orig_y_min
+    return [
+        np.float64(((orig_x - orig_x_min) / orig_x_range) * MORTON_CODE_VALUE_MAX).astype(np.uint32),
+        np.float64(((orig_y - orig_y_min) / orig_y_range) * MORTON_CODE_VALUE_MAX).astype(np.uint32),
+    ]
+
+# --------------------------
+# Quadtree / Z-interval helpers
+# --------------------------
+
+
+def intersects(ax0: int, ay0: int, ax1: int, ay1: int,
+               bx0: int, by0: int, bx1: int, by1: int) -> bool:
+    """Axis-aligned box intersection (inclusive integer bounds)."""
+    return not (ax1 < bx0 or bx1 < ax0 or ay1 < by0 or by1 < ay0)
+
+
+def contained(ix0: int, iy0: int, ix1: int, iy1: int,
+              ox0: int, oy0: int, ox1: int, oy1: int) -> bool:
+    """Is inner box entirely inside outer box? (inclusive integer bounds)"""
+    return (ox0 <= ix0 <= ix1 <= ox1) and (oy0 <= iy0 <= iy1 <= oy1)
+
+
+def point_inside(x: int, y: int, rx0: int, ry0: int, rx1: int, ry1: int) -> bool:
+    return (rx0 <= x <= rx1) and (ry0 <= y <= ry1)
+
+
+def cell_range(prefix: int, level: int, bits: int) -> Tuple[int, int]:
+    """
+    All Morton codes in a quadtree cell share the same prefix (2*level bits).
+    Fill the remaining lower bits with 0s (lo) or 1s (hi).
+    """
+    shift = 2 * (bits - level)
+    lo = prefix << shift
+    hi = ((prefix + 1) << shift) - 1
+    return lo, hi
+
+
+def merge_adjacent(intervals: List[Tuple[int, int]]) -> List[Tuple[int, int]]:
+    """Merge overlapping or directly adjacent intervals."""
+    if not intervals:
+        return []
+    intervals.sort(key=lambda t: t[0])
+    merged = [intervals[0]]
+    for lo, hi in intervals[1:]:
+        mlo, mhi = merged[-1]
+        if lo <= mhi + 1:
+            merged[-1] = (mlo, max(mhi, hi))
+        else:
+            merged.append((lo, hi))
+    return merged
+
+# --------------------------
+# Rectangle -> list of Morton intervals
+# --------------------------
+
+
+def zcover_rectangle(rx0: int, ry0: int, rx1: int, ry1: int, bits: int, stop_level: Optional[int] = None, merge: bool = True) -> List[Tuple[int, int]]:
+    """
+    Compute a (near-)minimal set of Morton code ranges covering the rectangle
+    [rx0..rx1] x [ry0..ry1] on an integer grid [0..2^bits-1]^2.
+
+    - If stop_level is None: exact cover (descend to exact containment).
+    - If stop_level is set (0..bits): stop descending at that level, adding
+      partially-overlapping cells as whole ranges (superset cover).
+    """
+    if not (0 <= rx0 <= rx1 <= (1 << bits) - 1 and 0 <= ry0 <= ry1 <= (1 << bits) - 1):
+        raise ValueError("Rectangle out of bounds for given bits.")
+
+    intervals: List[Tuple[int, int]] = []
+
+    # stack entries: (prefix, level, xmin, ymin, xmax, ymax)
+    stack = [(0, 0, 0, 0, (1 << bits) - 1, (1 << bits) - 1)]
+
+    while stack:
+        prefix, level, xmin, ymin, xmax, ymax = stack.pop()
+
+        if not intersects(xmin, ymin, xmax, ymax, rx0, ry0, rx1, ry1):
+            continue
+
+        # If we stop at this level for a loose cover, add full cell range.
+        if stop_level is not None and level == stop_level:
+            intervals.append(cell_range(prefix, level, bits))
+            continue
+
+        # Fully contained: add full cell range.
+        if contained(xmin, ymin, xmax, ymax, rx0, ry0, rx1, ry1):
+            intervals.append(cell_range(prefix, level, bits))
+            continue
+
+        # Leaf cell: single lattice point (only happens when level==bits)
+        if level == bits:
+            if point_inside(xmin, ymin, rx0, ry0, rx1, ry1):
+                intervals.append(cell_range(prefix, level, bits))
+            continue
+
+        # Otherwise, split into 4 children (Morton order: 00,01,10,11)
+        midx = (xmin + xmax) // 2
+        midy = (ymin + ymax) // 2
+
+        # q0: (x<=midx, y<=midy) -> child code 0b00
+        stack.append(((prefix << 2) | 0,
+                      level + 1,
+                      xmin, ymin, midx, midy))
+        # q1: (x>midx, y<=midy)  -> child code 0b01
+        stack.append(((prefix << 2) | 1,
+                      level + 1,
+                      midx + 1, ymin, xmax, midy))
+        # q2: (x<=midx, y>midy)  -> child code 0b10
+        stack.append(((prefix << 2) | 2,
+                      level + 1,
+                      xmin, midy + 1, midx, ymax))
+        # q3: (x>midx, y>midy)   -> child code 0b11
+        stack.append(((prefix << 2) | 3,
+                      level + 1,
+                      midx + 1, midy + 1, xmax, ymax))
+
+    return merge_adjacent(intervals) if merge else intervals
+
+
+# --------------------------
+# Morton intervals -> row ranges in a Morton-sorted column
+# --------------------------
+
+def zquery_rows_aux(morton_sorted: List[int], intervals: List[Tuple[int, int]], merge: bool = True) -> Tuple[List[Tuple[int, int]], List[int]]:
+    """
+    For each Z-interval [zlo, zhi], binary-search in the sorted Morton column
+    and return row index half-open ranges [i, j) to scan.
+    """
+
+    # Keep track of which keys were looked at during the binary searches.
+    # This is used for analysis / debugging, for instance, to enable
+    # evaluating how many HTTP requests would be needed in network-based case
+    # (which will also depend on Arrow row group size).
+    recorded_keys = []
+
+    def record_key_check(k: int) -> int:
+        # TODO: Does recorded_keys need to be marked as a global here?
+        recorded_keys.append(k)
+        return k
+
+    ranges: List[Tuple[int, int]] = []
+    # TODO: can these multiple binary searches be optimized?
+    # Since we are doing many searches in the same array, and in each search we learn where more elements are located.
+    for zlo, zhi in intervals:
+        i = bisect_left(morton_sorted, zlo, key=record_key_check)
+        # TODO: use lo=i in bisect_right to limit the search range?
+        # TODO: can the second binary search be further optimized since we just did a binary search via bisect_left?
+        j = bisect_right(morton_sorted, zhi, key=record_key_check)
+        if i < j:
+            ranges.append((i, j))
+
+    result = merge_adjacent(ranges) if merge else ranges
+    return result, recorded_keys
+
+
+def zquery_rows(morton_sorted: List[int], intervals: List[Tuple[int, int]], merge: bool = True) -> List[Tuple[int, int]]:
+    """
+    For each Z-interval [zlo, zhi], binary-search in the sorted Morton column
+    and return row index half-open ranges [i, j) to scan.
+    """
+    return zquery_rows_aux(morton_sorted, intervals, merge=merge)[0]
+
+
+def row_ranges_to_row_indices(intervals: List[Tuple[int, int]]) -> List[int]:
+    """
+    Convert row ranges [i, j) to a list of row indices.
+    Then, can index into pandas DataFrame using df.iloc[indices, :]
+    """
+    indices: List[int] = []
+    for i, j in intervals:
+        indices.extend(list(range(i, j)))
+    return indices
+
+
+# More helper functions.
+def sdata_points_process_columns(sdata, element, var_name_col=None, table_name=None) -> dd.DataFrame:
+    ddf = sdata.points[element]
+
+    if var_name_col is None:
+        # We can try to get it from the spatialdata_attrs metadata.
+        var_name_col = sdata.points[element].attrs["spatialdata_attrs"].get("feature_key")
+
+    # Appending codes for dictionary-encoded feature_name column.
+    if table_name is None and var_name_col is not None:
+        annotating_tables = get_element_annotators(sdata, element)
+        if len(annotating_tables) == 1:
+            table_name = annotating_tables[0]
+        elif len(annotating_tables) == 0:
+            raise ValueError(f"No annotating table found for Points element {element}, please specify table_name explicitly.")
+        else:
+            raise ValueError(f"Multiple annotating tables found for Points element {element}, please specify table_name explicitly.")
+
+    if var_name_col is not None:
+        var_df = sdata.tables[table_name].var
+        var_index = var_df.index.values.tolist()
+
+        def try_index(gene_name):
+            try:
+                return var_index.index(gene_name)
+            except BaseException:
+                return -1
+        ddf[f"{var_name_col}_codes"] = ddf[var_name_col].apply(try_index).astype('int32')
+
+    # Identify dictionary-encoded columns (categorical/string)
+    orig_columns = ddf.columns.tolist()
+    dict_encoded_cols = [col for col in orig_columns if pd.api.types.is_categorical_dtype(ddf[col].dtype) or pd.api.types.is_string_dtype(ddf[col].dtype)]
+
+    # Dictionary-encoded columns (i.e., categorical and string) must be stored as the rightmost columns of the dataframe.
+    ordered_columns = sorted(orig_columns, key=lambda colname: orig_columns.index(colname) if colname not in dict_encoded_cols else len(orig_columns))
+
+    # Reorder the columns of the dataframe
+    ddf = ddf[ordered_columns]
+
+    return ddf
+
+
+def sdata_points_write_bounding_box_attrs(sdata, element) -> dd.DataFrame:
+    ddf = sdata.points[element]
+
+    [x_min, x_max, y_min, y_max] = [ddf["x"].min().compute(), ddf["x"].max().compute(), ddf["y"].min().compute(), ddf["y"].max().compute()]
+    bounding_box = {
+        "x_min": float(x_min),
+        "x_max": float(x_max),
+        "y_min": float(y_min),
+        "y_max": float(y_max),
+    }
+
+    sdata_path = sdata.path
+    # TODO: error if no path
+
+    # Insert the bounding box as metadata for the sdata.points[element] Points element dataframe.
+    z = zarr.open(sdata_path, mode='a')
+    group = z[f'points/{element}']
+    group.attrs['bounding_box'] = bounding_box
+
+    # TODO: does anything special need to be done to ensure this is saved to disk?
+
+
+def sdata_points_modify_row_group_size(sdata, element, row_group_size: int = 50_000):
+    import pyarrow.parquet as pq
+
+    sdata_path = sdata.path
+    # TODO: error if no path
+
+    # List the parts of the parquet file.
+    parquet_path = join(sdata_path, "points", element, "points.parquet")
+
+    # Read the number of "part.*.parquet" files on disk.
+    part_files = [f for f in os.listdir(parquet_path) if f.startswith("part.") and f.endswith(".parquet")]
+    num_parts = len(part_files)
+
+    # Update the row group size in each .parquet file part.
+    for i in range(num_parts):
+        part_path = join(parquet_path, f"part.{i}.parquet")
+        table_read = pq.read_table(part_path)
+
+        # Write the table to a new Parquet file with the desired row group size.
+        pq.write_table(table_read, part_path, row_group_size=row_group_size)

vitessce/widget.py

@@ -181,7 +181,7 @@ const fallbackImportMap = {
         "react-dom": "https://cdn.vitessce.io/react-dom@18.2.0/index.js",
         "react-dom/client": "https://cdn.vitessce.io/react-dom@18.2.0/es2022/client.mjs",
         // Replaced with version-specific URL below.
-        "vitessce": "https://cdn.vitessce.io/vitessce@3.8.5/dist/index.min.js",
+        "vitessce": "https://cdn.vitessce.io/vitessce@VERSION/dist/index.min.js",
     },
 };
 /*
@@ -191,7 +191,7 @@ const fallbackDevImportMap = {
         "react-dom": "https://cdn.vitessce.io/react-dom@18.2.0/index_dev.js",
         "react-dom/client": "https://cdn.vitessce.io/react-dom@18.2.0/es2022/client.development.mjs",
         // Replaced with version-specific URL below.
-        "vitessce": "https://cdn.vitessce.io/@vitessce/dev@3.8.5/dist/index.js",
+        "vitessce": "https://cdn.vitessce.io/@vitessce/dev@VERSION/dist/index.js",
     },
 };
 */
@@ -729,7 +729,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     next_port = DEFAULT_PORT
 
-    js_package_version = Unicode('3.8.5').tag(sync=True)
+    js_package_version = Unicode('3.8.8').tag(sync=True)
     js_dev_mode = Bool(False).tag(sync=True)
     custom_js_url = Unicode('').tag(sync=True)
     plugin_esm = List(trait=Unicode(''), default_value=[]).tag(sync=True)
@@ -742,7 +742,7 @@ class VitessceWidget(anywidget.AnyWidget):
 
     store_urls = List(trait=Unicode(''), default_value=[]).tag(sync=True)
 
-    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.8.5', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
+    def __init__(self, config, height=600, theme='auto', uid=None, port=None, proxy=False, js_package_version='3.8.8', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, prefer_local=True, invoke_timeout=300000, invoke_batched=True, page_mode=False, page_esm=None, prevent_scroll=True, server_host=None):
         """
         Construct a new Vitessce widget. Not intended to be instantiated directly; instead, use ``VitessceConfig.widget``.
 
@@ -876,7 +876,7 @@ class VitessceWidget(anywidget.AnyWidget):
 # Launch Vitessce using plain HTML representation (no ipywidgets)
 
 
-def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.8.5', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
+def ipython_display(config, height=600, theme='auto', base_url=None, host_name=None, uid=None, port=None, proxy=False, js_package_version='3.8.8', js_dev_mode=False, custom_js_url='', plugins=None, remount_on_uid_change=True, page_mode=False, page_esm=None, server_host=None):
     from IPython.display import display, HTML
     uid_str = "vitessce" + get_uid_str(uid)
 

vitessce/wrappers.py

@@ -1432,6 +1432,10 @@ class SpatialDataWrapper(AnnDataWrapper):
         :type obs_segmentations_path: Optional[str]
         :param obs_points_path: Path to a points element, by default None
         :type obs_points_path: Optional[str]
+        :param str feature_labels_path: Path to a table var column containing feature labels (e.g., alternate gene symbols), instead of the default index column of the `var` dataframe.
+        :param list[str] obs_embedding_paths: Column names like `['obsm/X_umap', 'obsm/X_pca']` for showing scatterplots
+        :param list[str] obs_embedding_names: Overriding names like `['UMAP', 'PCA']` for displaying above scatterplots
+        :param list[str] obs_embedding_dims: Dimensions along which to get data for the scatterplot, like `[[0, 1], [4, 5]]` where `[0, 1]` is just the normal x and y but `[4, 5]` could be comparing the third and fourth principal components, for example.
         """
         raise_error_if_zero_or_more_than_one([
             sdata_path,
@@ -1551,6 +1555,7 @@ class SpatialDataWrapper(AnnDataWrapper):
             options = gen_sdata_obs_segmentations_schema(options, self._obs_segmentations_path, self._table_path, self._coordinate_system)
             options = gen_sdata_obs_points_schema(options, self._obs_points_path, self._table_path, self._coordinate_system)
             options = gen_feature_labels_schema(self._feature_labels, options)
+            options = gen_obs_embedding_schema(options, self._mappings_obsm, self._mappings_obsm_names, self._mappings_obsm_dims)
             if len(options.keys()) > 0:
                 obj_file_def = {
                     "fileType": ft.SPATIALDATA_ZARR_ZIP.value if self.is_zip else ft.SPATIALDATA_ZARR.value,

{vitessce-3.7.7.dist-info → vitessce-3.7.9.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: vitessce
-Version: 3.7.7
+Version: 3.7.9
 Summary: Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce
 Project-URL: repository, https://github.com/vitessce/vitessce-python
 Author-email: Mark Keller <mark_keller@hms.harvard.edu>

{vitessce-3.7.7.dist-info → vitessce-3.7.9.dist-info}/RECORD

@@ -8,17 +8,18 @@ vitessce/repr.py,sha256=qMmefmZ3E-3sRVxeI5q1DTZnfuwbXKiA85eyqk5MCT4,2287
 vitessce/responses.py,sha256=Z6Wo4AXN-RyzmxMPhSuhpIsHTItHM4GyIgMLGoVEYcU,339
 vitessce/routes.py,sha256=U8T-L-3QCD_tAbPF8LsUlSMhPWNbyzbLNUnxP9Z9s9o,2140
 vitessce/utils.py,sha256=obzjj65qsagu60_yuhGc-0jmHO-BW0Y-bDs0FgrBqLY,981
-vitessce/widget.py,sha256=ndgKqwNLrgYnXnA5pGCu2mgQe0_vF1ZMedWuHDYqPpo,39260
-vitessce/wrappers.py,sha256=WdOQ9w4ElGZH_nKrZAfyrtHxW3iVDzIQ1eqBPlrucj0,76993
-vitessce/data_utils/__init__.py,sha256=3mWi1lMjoj4_dNbhMOvyE-HEJu0qpMzcmkhfz_5T6n8,361
+vitessce/widget.py,sha256=MSnNsYWwy2XjKjm3xp8ycw8Ds5swC61dGucseQVM-PY,39264
+vitessce/wrappers.py,sha256=UBUc2lbN3b0G31ZyE3XAxMlaFI3PKKAvv9KuuExxaEA,77804
+vitessce/data_utils/__init__.py,sha256=lZZ58HlbMiWYIBw3JckGorjmySR_8N4RCZS3U00jUsQ,716
 vitessce/data_utils/anndata.py,sha256=iLa5-bRezHgBzL_XCHO7w0pc0RQ4urzZbDsqJbBYeCk,10668
 vitessce/data_utils/entities.py,sha256=X8enC_TQbgwBzjgD1x53IPS6aVr9wyP0s-NLuYBeMeU,11705
 vitessce/data_utils/multivec.py,sha256=YVc68uKNdS-ga89GapQjY9lDjmje0dm-MExq1yT_6ZE,11571
 vitessce/data_utils/ome.py,sha256=te1X933QTRfCm8N5uVXZREShtxDdAEggZZKKEoJdlhU,5518
+vitessce/data_utils/spatialdata_points_zorder.py,sha256=pAga1GGyiFgvJCxiqjpsqDpVpPfR5kmLWs3drMAm5Sc,19281
 vitessce/widget_plugins/__init__.py,sha256=lto2GXnc7KwjIoT-jvzyRYLj0XTJG3uxoX45Hc9EcWA,82
 vitessce/widget_plugins/demo_plugin.py,sha256=14S7nOxdlKSxIHw9DUcNCN83NE_U1EMPy2D4k0FDues,1797
 vitessce/widget_plugins/spatial_query.py,sha256=CYxvmMT1Je_jguikPROQxlegkPgIIzemKGbZSJfZMyI,12314
-vitessce-3.7.7.dist-info/METADATA,sha256=iXdHIIrXmQc6KTomDoFxfYRq20FRbN43WYOp46QZ1gY,9826
-vitessce-3.7.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-vitessce-3.7.7.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
-vitessce-3.7.7.dist-info/RECORD,,
+vitessce-3.7.9.dist-info/METADATA,sha256=9xaMY_hnKOoyZ_CylmhK-PCPwVFiuuNZNX4ocMusw8U,9826
+vitessce-3.7.9.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+vitessce-3.7.9.dist-info/licenses/LICENSE,sha256=sNNpI0PQ57AW8_XnTAjU5Yw8YBA_DRNkVHrHYpCIhRU,1067
+vitessce-3.7.9.dist-info/RECORD,,