From 7b0a239b9f17cbd416063863c82ca52ade00a02e Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Tue, 20 Oct 2020 14:37:10 +0200
Subject: [PATCH 1/2] HCS: add Plate spec

---
 ome_zarr/reader.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/ome_zarr/reader.py b/ome_zarr/reader.py
index 2cd93a7b..1261eae5 100644
--- a/ome_zarr/reader.py
+++ b/ome_zarr/reader.py
@@ -2,6 +2,7 @@
 
 import logging
 from abc import ABC
+from string import ascii_uppercase
 from typing import Any, Dict, Iterator, List, Optional, Type, Union, cast
 
 import dask.array as da
@@ -48,6 +49,8 @@ def __init__(
             self.specs.append(Multiscales(self))
         if OMERO.matches(zarr):
             self.specs.append(OMERO(self))
+        if Plate.matches(zarr):
+            self.specs.append(Plate(self))
 
     @property
     def visible(self) -> bool:
@@ -336,6 +339,34 @@ def __init__(self, node: Node) -> None:
             LOGGER.error(f"failed to parse metadata: {e}")
 
 
+class Plate(Spec):
+    @staticmethod
+    def matches(zarr: BaseZarrLocation) -> bool:
+        return bool("plate" in zarr.root_attrs)
+
+    def __init__(self, node: Node) -> None:
+        super().__init__(node)
+        # TODO: start checking metadata version
+        self.plate_data = self.lookup("plate", {})
+        self.rows = self.plate_data.get("rows", 0)
+        self.cols = self.plate_data.get("columns", 0)
+
+        # FIXME: shouldn't hard code
+        self.acquisitions = ["PlateAcquisition Name 0"]
+        self.fields = ["Field_1"]
+        self.row_labels = ascii_uppercase[0 : self.rows]
+        self.col_labels = range(1, self.cols + 1)
+
+        for acq in self.acquisitions:
+            for row in self.row_labels:
+                for col in self.col_labels:
+                    for field in self.fields:
+                        path = f"{acq}/{row}/{col}/{field}"
+                        child_zarr = self.zarr.create(path)
+                        if child_zarr.exists():
+                            node.add(child_zarr, visibility=True)
+
+
 class Reader:
     """Parses the given Zarr instance into a collection of Nodes properly ordered
     depending on context.

From c9f4901ff42519910c6e87ebd25d715bedad6547 Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Wed, 21 Oct 2020 09:22:51 +0200
Subject: [PATCH 2/2] HCS: only first field is visible

---
 ome_zarr/reader.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/ome_zarr/reader.py b/ome_zarr/reader.py
index 1261eae5..32df81e6 100644
--- a/ome_zarr/reader.py
+++ b/ome_zarr/reader.py
@@ -353,10 +353,11 @@ def __init__(self, node: Node) -> None:
 
         # FIXME: shouldn't hard code
         self.acquisitions = ["PlateAcquisition Name 0"]
-        self.fields = ["Field_1"]
+        self.fields = ["Field_1", "Field_2", "Field_3", "Field_4"]
         self.row_labels = ascii_uppercase[0 : self.rows]
         self.col_labels = range(1, self.cols + 1)
 
+        visibility = True
         for acq in self.acquisitions:
             for row in self.row_labels:
                 for col in self.col_labels:
@@ -364,7 +365,8 @@ def __init__(self, node: Node) -> None:
                         path = f"{acq}/{row}/{col}/{field}"
                         child_zarr = self.zarr.create(path)
                         if child_zarr.exists():
-                            node.add(child_zarr, visibility=True)
+                            node.add(child_zarr, visibility=visibility)
+                            visibility = False
 
 
 class Reader: