rarrange code

janelia-cellmap · Feb 9, 2024 · f722326 · f722326
1 parent 150b293
commit f722326
Showing 1 changed file with 47 additions and 44 deletions.
diff --git a/examples/distance_task/finetune_liver.ipynb b/examples/distance_task/finetune_liver.ipynb
@@ -29,8 +29,7 @@
     "    ResampledArrayConfig,\n",
     "    ZarrArrayConfig,\n",
     ")\n",
-    "from dacapo.experiments.datasplits.datasets import RawGTDatasetConfig\n",
-    "from dacapo.experiments.datasplits import TrainValidateDataSplitConfig\n",
+    "from dacapo.experiments.tasks import DistanceTaskConfig\n",
     "from dacapo.experiments.architectures import CNNectomeUNetConfig\n",
     "from dacapo.experiments.trainers import GunpowderTrainerConfig\n",
     "from dacapo.experiments.trainers.gp_augments import (\n",
@@ -39,7 +38,10 @@
     "    IntensityAugmentConfig,\n",
     "    IntensityScaleShiftAugmentConfig,\n",
     ")\n",
-    "from dacapo.experiments.tasks import DistanceTaskConfig"
+    "from dacapo.experiments.datasplits import TrainValidateDataSplitConfig\n",
+    "from dacapo.experiments.datasplits.datasets import RawGTDatasetConfig\n",
+    "from dacapo.experiments.starts import StartConfig\n",
+    "from dacapo.experiments import RunConfig"
    ]
   },
   {
@@ -82,6 +84,36 @@
   },
   {
    "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Architecture"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "architecture_config = CNNectomeUNetConfig(\n",
+    "    name=\"example_upsample-unet\",\n",
+    "    input_shape=(216, 216, 216),\n",
+    "    fmaps_out=72,\n",
+    "    fmaps_in=1,\n",
+    "    num_fmaps=12,\n",
+    "    fmap_inc_factor=6,\n",
+    "    downsample_factors=[(2, 2, 2), (3, 3, 3), (3, 3, 3)],\n",
+    "    kernel_size_down=None,\n",
+    "    kernel_size_up=None,\n",
+    "    eval_shape_increase=(72, 72, 72),\n",
+    "    upsample_factors=[(2, 2, 2)],\n",
+    "    constant_upsample=True,\n",
+    "    padding=\"valid\",\n",
+    ")"
+   ]
+  },
+  {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
@@ -90,7 +122,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -118,37 +150,6 @@
     ")"
    ]
   },
-  {
-   "attachments": {},
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Architecture"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 4,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "architecture_config = CNNectomeUNetConfig(\n",
-    "    name=\"example_upsample-unet\",\n",
-    "    input_shape=(216, 216, 216),\n",
-    "    fmaps_out=72,\n",
-    "    fmaps_in=1,\n",
-    "    num_fmaps=12,\n",
-    "    fmap_inc_factor=6,\n",
-    "    downsample_factors=[(2, 2, 2), (3, 3, 3), (3, 3, 3)],\n",
-    "    kernel_size_down=None,\n",
-    "    kernel_size_up=None,\n",
-    "    eval_shape_increase=(72, 72, 72),\n",
-    "    upsample_factors=[(2, 2, 2)],\n",
-    "    constant_upsample=True,\n",
-    "    padding=\"valid\",\n",
-    ")"
-   ]
-  },
   {
    "attachments": {},
    "cell_type": "markdown",
@@ -1638,15 +1639,10 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
-    "from dacapo.experiments import RunConfig\n",
-    "from dacapo.experiments.starts import StartConfig\n",
-    "from dacapo.store.create_store import create_config_store\n",
-    "\n",
-    "config_store = create_config_store()\n",
     "start_config = StartConfig(\n",
     "    \"finetuned_3d_lsdaffs_nuclearpores_6-28_weights_upsample-unet_default_v2_weights__test_3\",\n",
     "    \"145000\",\n",
@@ -1661,16 +1657,16 @@
     "                \"example\",\n",
     "                \"scratch\" if start_config is None else \"finetuned\",\n",
     "                task_config.name,\n",
-    "                datasplit_config.name,\n",
     "                architecture_config.name,\n",
     "                trainer_config.name,\n",
+    "                datasplit_config.name,\n",
     "            ]\n",
     "        )\n",
     "        + f\"__{i}\",\n",
     "        task_config=task_config,\n",
-    "        datasplit_config=datasplit_config,\n",
     "        architecture_config=architecture_config,\n",
     "        trainer_config=trainer_config,\n",
+    "        datasplit_config=datasplit_config,\n",
     "        num_iterations=iterations,\n",
     "        validation_interval=validation_interval,\n",
     "        repetition=i,\n",
@@ -1687,7 +1683,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1700,6 +1696,13 @@
     "config_store.store_datasplit_config(datasplit_config)\n",
     "config_store.store_run_config(run_config)"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {