From 3a62e2a30f44b6bdcb121112a9db18c32d5f938e Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <sneakers-the-rat@protonmail.com>
Date: Mon, 11 Nov 2024 23:59:06 -0800
Subject: [PATCH] rm sdcard formats

---
 miniscope_io/formats/__init__.py |  4 ---
 miniscope_io/formats/sdcard.py   | 51 --------------------------------
 notebooks/Wire-Free-DAQ.ipynb    | 12 ++++----
 notebooks/grab_frames.ipynb      |  6 ++--
 tests/test_formats.py            |  3 +-
 5 files changed, 9 insertions(+), 67 deletions(-)
 delete mode 100644 miniscope_io/formats/sdcard.py

diff --git a/miniscope_io/formats/__init__.py b/miniscope_io/formats/__init__.py
index 5ab7fe30..a1833181 100644
--- a/miniscope_io/formats/__init__.py
+++ b/miniscope_io/formats/__init__.py
@@ -3,7 +3,3 @@
 that describe fixed per-device configurations for the generic config
 models in :mod:`~.miniscope_io.models.stream` et al.
 """
-
-from miniscope_io.formats.sdcard import WireFreeSDLayout, WireFreeSDLayout_Battery
-
-__all__ = ["WireFreeSDLayout", "WireFreeSDLayout_Battery"]
diff --git a/miniscope_io/formats/sdcard.py b/miniscope_io/formats/sdcard.py
deleted file mode 100644
index 006363e3..00000000
--- a/miniscope_io/formats/sdcard.py
+++ /dev/null
@@ -1,51 +0,0 @@
-"""
-SD Card data layout formats for different miniscopes!
-"""
-
-from miniscope_io.models.sdcard import (
-    ConfigPositions,
-    SDBufferHeaderFormat,
-    SDHeaderPositions,
-    SDLayout,
-    SectorConfig,
-)
-
-WireFreeSDLayout = SDLayout(
-    version="0.1.1",
-    sectors=SectorConfig(header=1022, config=1023, data=1024, size=512),
-    write_key0=0x0D7CBA17,
-    write_key1=0x0D7CBA17,
-    write_key2=0x0D7CBA17,
-    write_key3=0x0D7CBA17,
-    header=SDHeaderPositions(
-        gain=4, led=5, ewl=6, record_length=7, fs=8, delay_start=9, battery_cutoff=10
-    ),
-    config=ConfigPositions(
-        width=0,
-        height=1,
-        fs=2,
-        buffer_size=3,
-        n_buffers_recorded=4,
-        n_buffers_dropped=5,
-    ),
-    buffer=SDBufferHeaderFormat(
-        length=0,
-        linked_list=1,
-        frame_num=2,
-        buffer_count=3,
-        frame_buffer_count=4,
-        write_buffer_count=5,
-        dropped_buffer_count=6,
-        timestamp=7,
-        data_length=8,
-    ),
-)
-
-WireFreeSDLayout_Battery = SDLayout(**WireFreeSDLayout.model_dump())
-"""
-Making another format for now, but added version field so that we could
-replace making more top-level classes with a FormatCollection that can store 
-sets of formats for the same device with multiple versions.
-"""
-WireFreeSDLayout_Battery.buffer.write_timestamp = 9
-WireFreeSDLayout_Battery.buffer.battery_voltage = 10
diff --git a/notebooks/Wire-Free-DAQ.ipynb b/notebooks/Wire-Free-DAQ.ipynb
index ff96fb3d..11c06957 100644
--- a/notebooks/Wire-Free-DAQ.ipynb
+++ b/notebooks/Wire-Free-DAQ.ipynb
@@ -156,10 +156,10 @@
      "ename": "ValueError",
      "evalue": "read length must be non-negative or -1",
      "traceback": [
-      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
-      "\u001b[1;31mValueError\u001b[0m                                Traceback (most recent call last)",
-      "\u001b[1;32m<ipython-input-12-6f1c87781fe0>\u001b[0m in \u001b[0;36m<module>\u001b[1;34m\u001b[0m\n\u001b[0;32m      7\u001b[0m \u001b[1;32mfor\u001b[0m \u001b[0mi\u001b[0m \u001b[1;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m5000\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m:\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m      8\u001b[0m     \u001b[0mdataHeader\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfromstring\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mf\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;36m4\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0muint32\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[1;32m----> 9\u001b[1;33m     \u001b[0mdataHeader\u001b[0m \u001b[1;33m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mappend\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdataHeader\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mfromstring\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mf\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0mread\u001b[0m\u001b[1;33m(\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdataHeader\u001b[0m\u001b[1;33m[\u001b[0m\u001b[0mBUFFER_HEADER_HEADER_LENGTH_POS\u001b[0m\u001b[1;33m]\u001b[0m \u001b[1;33m-\u001b[0m \u001b[1;36m1\u001b[0m\u001b[1;33m)\u001b[0m \u001b[1;33m*\u001b[0m \u001b[1;36m4\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m,\u001b[0m \u001b[0mdtype\u001b[0m\u001b[1;33m=\u001b[0m\u001b[0mnp\u001b[0m\u001b[1;33m.\u001b[0m\u001b[0muint32\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0m\u001b[0;32m     10\u001b[0m \u001b[1;33m\u001b[0m\u001b[0m\n\u001b[0;32m     11\u001b[0m     \u001b[0mprint\u001b[0m\u001b[1;33m(\u001b[0m\u001b[0mdataHeader\u001b[0m\u001b[1;33m)\u001b[0m\u001b[1;33m\u001b[0m\u001b[1;33m\u001b[0m\u001b[0m\n",
-      "\u001b[1;31mValueError\u001b[0m: read length must be non-negative or -1"
+      "\u001B[1;31m---------------------------------------------------------------------------\u001B[0m",
+      "\u001B[1;31mValueError\u001B[0m                                Traceback (most recent call last)",
+      "\u001B[1;32m<ipython-input-12-6f1c87781fe0>\u001B[0m in \u001B[0;36m<module>\u001B[1;34m\u001B[0m\n\u001B[0;32m      7\u001B[0m \u001B[1;32mfor\u001B[0m \u001B[0mi\u001B[0m \u001B[1;32min\u001B[0m \u001B[0mrange\u001B[0m\u001B[1;33m(\u001B[0m\u001B[1;36m5000\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m:\u001B[0m\u001B[1;33m\u001B[0m\u001B[1;33m\u001B[0m\u001B[0m\n\u001B[0;32m      8\u001B[0m     \u001B[0mdataHeader\u001B[0m \u001B[1;33m=\u001B[0m \u001B[0mnp\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0mfromstring\u001B[0m\u001B[1;33m(\u001B[0m\u001B[0mf\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0mread\u001B[0m\u001B[1;33m(\u001B[0m\u001B[1;36m4\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m,\u001B[0m \u001B[0mdtype\u001B[0m\u001B[1;33m=\u001B[0m\u001B[0mnp\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0muint32\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m\u001B[0m\u001B[1;33m\u001B[0m\u001B[0m\n\u001B[1;32m----> 9\u001B[1;33m     \u001B[0mdataHeader\u001B[0m \u001B[1;33m=\u001B[0m \u001B[0mnp\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0mappend\u001B[0m\u001B[1;33m(\u001B[0m\u001B[0mdataHeader\u001B[0m\u001B[1;33m,\u001B[0m \u001B[0mnp\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0mfromstring\u001B[0m\u001B[1;33m(\u001B[0m\u001B[0mf\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0mread\u001B[0m\u001B[1;33m(\u001B[0m\u001B[1;33m(\u001B[0m\u001B[0mdataHeader\u001B[0m\u001B[1;33m[\u001B[0m\u001B[0mBUFFER_HEADER_HEADER_LENGTH_POS\u001B[0m\u001B[1;33m]\u001B[0m \u001B[1;33m-\u001B[0m \u001B[1;36m1\u001B[0m\u001B[1;33m)\u001B[0m \u001B[1;33m*\u001B[0m \u001B[1;36m4\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m,\u001B[0m \u001B[0mdtype\u001B[0m\u001B[1;33m=\u001B[0m\u001B[0mnp\u001B[0m\u001B[1;33m.\u001B[0m\u001B[0muint32\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m\u001B[0m\u001B[1;33m\u001B[0m\u001B[0m\n\u001B[0m\u001B[0;32m     10\u001B[0m \u001B[1;33m\u001B[0m\u001B[0m\n\u001B[0;32m     11\u001B[0m     \u001B[0mprint\u001B[0m\u001B[1;33m(\u001B[0m\u001B[0mdataHeader\u001B[0m\u001B[1;33m)\u001B[0m\u001B[1;33m\u001B[0m\u001B[1;33m\u001B[0m\u001B[0m\n",
+      "\u001B[1;31mValueError\u001B[0m: read length must be non-negative or -1"
      ]
     }
    ],
@@ -239,7 +239,7 @@
    "outputs": [],
    "source": [
     "# Delete data from SD Card\n",
-    "f.seek(ataStartSector * sectorSize, 0)\n",
+    "f.seek(dataStartSector * sectorSize, 0)\n",
     "\n",
     "zeros = []\n",
     "for i in range(512):\n",
@@ -249,4 +249,4 @@
    ]
   }
  ]
-}
\ No newline at end of file
+}
diff --git a/notebooks/grab_frames.ipynb b/notebooks/grab_frames.ipynb
index 06c22a89..6c33874e 100644
--- a/notebooks/grab_frames.ipynb
+++ b/notebooks/grab_frames.ipynb
@@ -33,7 +33,7 @@
     "warnings.filterwarnings(\"ignore\")\n",
     "\n",
     "from miniscope_io.io import SDCard\n",
-    "from miniscope_io.formats import WireFreeSDLayout"
+    "from miniscope_io.models.sdcard import SDLayout"
    ]
   },
   {
@@ -100,9 +100,7 @@
      ]
     }
    ],
-   "source": [
-    "pprint(WireFreeSDLayout.dict(), sort_dicts=False)"
-   ]
+   "source": "pprint(SDLayout.from_id('wirefree-sd-layout'), sort_dicts=False)"
   },
   {
    "cell_type": "markdown",
diff --git a/tests/test_formats.py b/tests/test_formats.py
index 9ac437a6..3930c2aa 100644
--- a/tests/test_formats.py
+++ b/tests/test_formats.py
@@ -4,12 +4,11 @@
 import json
 import importlib
 
-from miniscope_io.formats import WireFreeSDLayout
 from miniscope_io.models.sdcard import SDLayout
 
 
 # More formats can be added here as needed.
-@pytest.mark.parametrize("format", [WireFreeSDLayout])
+@pytest.mark.parametrize("format", [SDLayout.from_id("wirefree-sd-layout")])
 def test_to_from_json(format):
     """
     A format can be exported and re-imported from JSON and remain equivalent