Atlas metadata print out (#91)

* printing metadata

* merged latest PR

* black

* requirement update

* moved to utils + core

bg_atlasapi/bg_atlas.py

@@ -1,9 +1,9 @@
 from pathlib import Path
 import tarfile
 import requests
-
 from rich import print as rprint
 
+
 from bg_atlasapi import utils, config, core, descriptors
 
 
@@ -179,13 +179,3 @@ def check_latest_version(self):
  )
  return False
  return True
-
- def __repr__(self):
- """Fancy print for the atlas providing authors information."""
- meta = self.metadata
- name_split = self.atlas_name.split("_")
- pretty_name = "{} {} atlas (res. {})".format(*name_split)
- pretty_string = (
- f"{pretty_name}\nFrom: {meta['atlas_link']} ({meta['citation']} )"
- )
- return pretty_string

bg_atlasapi/core.py

@@ -3,10 +3,12 @@
 import numpy as np
 from collections import UserDict
 import warnings
+from rich.console import Console
+from io import StringIO
 
 from bg_space import AnatomicalSpace
 
-from bg_atlasapi.utils import read_json, read_tiff
+from bg_atlasapi.utils import read_json, read_tiff, _rich_atlas_metadata
 from bg_atlasapi.structure_class import StructuresDict
 from bg_atlasapi.descriptors import (
  METADATA_FILENAME,
@@ -70,6 +72,35 @@ def __init__(self, path):
  self._hemispheres = None
  self._lookup = None
 
+ def __repr__(self):
+ """Fancy print for the atlas providing authors information."""
+ name_split = self.atlas_name.split("_")
+ pretty_name = "{} {} atlas (res. {})".format(*name_split)
+ return pretty_name
+
+ def __str__(self):
+ """
+ If the atlas metadat are to be printed
+ with the built in print function instead of rich's, then
+ print the rich panel as a string.
+
+ It will miss the colors.
+
+ """
+ buf = StringIO()
+ _console = Console(file=buf, force_jupyter=False)
+ _console.print(self)
+
+ return buf.getvalue()
+
+ def __rich_console__(self, *args):
+ """
+ Method for rich API's console protocol.
+ Prints the atlas metadata as a table nested in a panel
+ """
+ panel = _rich_atlas_metadata(self.atlas_name, self.metadata)
+ yield panel
+
  @property
  def resolution(self):
  """Make resolution more accessible from class."""

bg_atlasapi/utils.py

@@ -11,10 +11,62 @@
  TimeRemainingColumn,
  Progress,
 )
+from rich.table import Table
+from rich.panel import Panel
+from rich.pretty import Pretty
+from rich.text import Text
 
 logging.getLogger("urllib3").setLevel(logging.WARNING)
 
 
+def _rich_atlas_metadata(atlas_name, metadata):
+ orange = "#f59e42"
+ dimorange = "#b56510"
+ gray = "#A9A9A9"
+ mocassin = "#FFE4B5"
+ cit_name, cit_link = metadata["citation"].split(", ")
+
+ # Create a rich table
+ tb = Table(
+ box=None,
+ show_lines=False,
+ title=atlas_name.replace("_", " ").capitalize(),
+ title_style=f"bold {orange}",
+ )
+
+ # Add entries to table
+ tb.add_column(
+ style=f"bold {mocassin}",
+ justify="right",
+ min_width=8,
+ max_width=40,
+ )
+ tb.add_column(min_width=20, max_width=48)
+
+ tb.add_row(
+ "name:",
+ Text.from_markup(
+ metadata["name"] + f' [{gray}](v{metadata["version"]})'
+ ),
+ )
+ tb.add_row("species:", Text.from_markup(f'[i]{metadata["species"]}'))
+ tb.add_row("citation:", Text.from_markup(f"{cit_name} [{gray}]{cit_link}"))
+ tb.add_row("link:", Text.from_markup(metadata["atlas_link"]))
+
+ tb.add_row("")
+ tb.add_row(
+ "orientation:",
+ Text.from_markup(f"[bold]{metadata['orientation']}"),
+ )
+ tb.add_row("symmetric:", Pretty(metadata["symmetric"]))
+ tb.add_row("resolution:", Pretty(metadata["resolution"]))
+ tb.add_row("shape:", Pretty(metadata["shape"]))
+
+ # Fit into panel and yield
+ panel = Panel.fit(tb, border_style=dimorange)
+ return panel
+
+
 def atlas_repr_from_name(name):
  """Generate dictionary with atlas description given the name."""
  parts = name.split("_")

requirements.txt

@@ -5,5 +5,5 @@ pandas
 requests
 meshio
 click
-rich>=8.0.0
+rich>=9.0.0
 bg-space>=0.5.0