Merge bd5a7b4 into b563b6b

angelolab · Nov 16, 2022 · 291017f · 291017f
2 parents b563b6b + bd5a7b4
commit 291017f
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Showing 3 changed files with 50 additions and 52 deletions.
diff --git a/templates/2_Cluster_Pixels.ipynb b/templates/2_Cluster_Pixels.ipynb
@@ -687,7 +687,7 @@
    "outputs": [],
    "source": [
     "# select fovs to display\n",
-    "pixel_fovs = ['fov0', 'fov1']"
+    "subset_pixel_fovs = ['fov0', 'fov1']"
    ]
   },
   {
@@ -710,10 +710,9 @@
     "        img_sub_folder, io_utils.list_files(os.path.join(tiff_dir, fovs[0], img_sub_folder), substrs=['.tiff'])[0]\n",
     "    )\n",
     "\n",
-    "# generate and save the pixel cluster masks for each fov in pixel_fovs\n",
-    "\n",
+    "# generate and save the pixel cluster masks for each fov in subset_pixel_fovs\n",
     "data_utils.generate_and_save_pixel_cluster_masks(\n",
-    "    fovs=pixel_fovs,\n",
+    "    fovs=subset_pixel_fovs,\n",
     "    base_dir=base_dir,\n",
     "    save_dir=os.path.join(base_dir, pixel_output_dir),\n",
     "    tiff_dir=tiff_dir,\n",
@@ -793,23 +792,22 @@
     }
    ],
    "source": [
-    "subset_pixel_fovs = pixel_fovs\n",
-    "\n",
-    "pixel_cluster_masks = load_utils.load_imgs_from_dir(\n",
-    "    data_dir = os.path.join(base_dir, pixel_output_dir, \"pixel_masks\"),\n",
-    "    files=[f + \"_pixel_mask.tiff\" for f in subset_pixel_fovs],\n",
-    "    trim_suffix=\"_pixel_mask\",\n",
-    "    match_substring=\"_pixel_mask\",\n",
-    "    xr_dim_name=\"pixel_mask\",\n",
-    "    xr_channel_names=None,\n",
-    ")\n",
+    "for pixel_fov in subset_pixel_fovs:\n",
+    "    pixel_cluster_mask = load_utils.load_imgs_from_dir(\n",
+    "        data_dir=os.path.join(base_dir, pixel_output_dir, \"pixel_masks\"),\n",
+    "        files=[pixel_fov + \"_pixel_mask.tiff\"],\n",
+    "        trim_suffix=\"_pixel_mask\",\n",
+    "        match_substring=\"_pixel_mask\",\n",
+    "        xr_dim_name=\"pixel_mask\",\n",
+    "        xr_channel_names=None,\n",
+    "    )\n",
     "\n",
-    "plot_utils.plot_pixel_cell_cluster_overlay(\n",
-    "    pixel_cluster_masks,\n",
-    "    pixel_fovs,\n",
-    "    os.path.join(base_dir, pixel_meta_cluster_remap_name),\n",
-    "    metacluster_colors=raw_cmap\n",
-    ")"
+    "    plot_utils.plot_pixel_cell_cluster_overlay(\n",
+    "        pixel_cluster_mask,\n",
+    "        [pixel_fov],\n",
+    "        os.path.join(base_dir, pixel_meta_cluster_remap_name),\n",
+    "        metacluster_colors=raw_cmap\n",
+    "    )"
    ]
   },
   {
@@ -882,7 +880,7 @@
    "outputs": [],
    "source": [
     "plot_utils.create_mantis_dir(\n",
-    "    fovs=pixel_fovs,\n",
+    "    fovs=subset_pixel_fovs,\n",
     "    mantis_project_path=os.path.join(base_dir, pixel_output_dir, \"mantis\"),\n",
     "    img_data_path=tiff_dir,\n",
     "    mask_output_dir=os.path.join(base_dir, pixel_output_dir, \"pixel_masks\"),\n",

diff --git a/templates/3_Cluster_Cells.ipynb b/templates/3_Cluster_Cells.ipynb
@@ -615,7 +615,7 @@
    "outputs": [],
    "source": [
     "# select fovs to display\n",
-    "cell_fovs = ['fov0', 'fov1']"
+    "subset_cell_fovs = ['fov0', 'fov1']"
    ]
   },
   {
@@ -628,9 +628,9 @@
    },
    "outputs": [],
    "source": [
-    "# generate and save the cell cluster masks for each fov in cell_fovs\n",
+    "# generate and save the cell cluster masks for each fov in subset_cell_fovs\n",
     "data_utils.generate_and_save_cell_cluster_masks(\n",
-    "    fovs=cell_fovs,\n",
+    "    fovs=subset_cell_fovs,\n",
     "    base_dir=base_dir,\n",
     "    save_dir=os.path.join(base_dir, \"pixie\", cell_output_dir),\n",
     "    seg_dir=os.path.join(base_dir, segmentation_dir, \"deepcell_output\"),\n",
@@ -658,23 +658,22 @@
    },
    "outputs": [],
    "source": [
-    "subset_cell_fovs = cell_fovs\n",
+    "for cell_fov in subset_cell_fovs:\n",
+    "    cell_cluster_mask = load_utils.load_imgs_from_dir(\n",
+    "        data_dir = os.path.join(base_dir, \"pixie\", cell_output_dir, \"cell_masks\"),\n",
+    "        files=[cell_fov + \"_cell_mask.tiff\"],\n",
+    "        trim_suffix=\"_cell_mask\",\n",
+    "        match_substring=\"_cell_mask\",\n",
+    "        xr_dim_name=\"cell_mask\",\n",
+    "        xr_channel_names=None,\n",
+    "    )\n",
     "\n",
-    "cell_cluster_masks = load_utils.load_imgs_from_dir(\n",
-    "    data_dir = os.path.join(base_dir, \"pixie\", cell_output_dir, \"cell_masks\"),\n",
-    "    files=[f + \"_cell_mask.tiff\" for f in subset_cell_fovs],\n",
-    "    trim_suffix=\"_cell_mask\",\n",
-    "    match_substring=\"_cell_mask\",\n",
-    "    xr_dim_name=\"cell_mask\",\n",
-    "    xr_channel_names=None,\n",
-    ")\n",
-    "\n",
-    "plot_utils.plot_pixel_cell_cluster_overlay(\n",
-    "    cell_cluster_masks,\n",
-    "    cell_fovs,\n",
-    "    os.path.join(base_dir, cell_meta_cluster_remap_name),\n",
-    "    metacluster_colors=raw_cmap\n",
-    ")"
+    "    plot_utils.plot_pixel_cell_cluster_overlay(\n",
+    "        cell_cluster_mask,\n",
+    "        [cell_fov],\n",
+    "        os.path.join(base_dir, cell_meta_cluster_remap_name),\n",
+    "        metacluster_colors=raw_cmap\n",
+    "    )"
    ]
   },
   {
@@ -726,7 +725,7 @@
    "outputs": [],
    "source": [
     "plot_utils.create_mantis_dir(\n",
-    "    fovs=cell_fovs,\n",
+    "    fovs=subset_cell_fovs,\n",
     "    mantis_project_path=os.path.join(base_dir, \"pixie\", cell_output_dir, \"mantis\"),\n",
     "    img_data_path=tiff_dir,\n",
     "    mask_output_dir=os.path.join(base_dir, \"pixie\", cell_output_dir, \"cell_masks\"),\n",

diff --git a/templates/example_neighborhood_analysis_script.ipynb b/templates/example_neighborhood_analysis_script.ipynb
@@ -457,11 +457,11 @@
    "outputs": [],
    "source": [
     "# select fovs to display\n",
-    "fovs = ['fov6']\n",
+    "subset_neighborhood_fovs = ['fov6']\n",
     "\n",
     "# generate and save the neighborhood masks for the fovs to display\n",
     "data_utils.generate_and_save_neighborhood_cluster_masks(\n",
-    "    fovs,\n",
+    "    subset_neighborhood_fovs,\n",
     "    overlay_out_dir,\n",
     "    all_data_cluster_labeled,\n",
     "    seg_output,\n",
@@ -487,16 +487,17 @@
    ],
    "source": [
     "# load the masks in and plot them\n",
-    "neighborhood_masks = load_utils.load_imgs_from_dir(\n",
-    "    data_dir=overlay_out_dir,\n",
-    "    files=[f + \"_neighborhood_mask.tiff\" for f in fovs],\n",
-    "    trim_suffix=\"_neighborhood_mask\",\n",
-    "    match_substring=\"_neighborhood_mask\",\n",
-    "    xr_dim_name=\"neighborhood_mask\",\n",
-    "    xr_channel_names=None,\n",
-    ")\n",
+    "for fov in subset_neighborhood_fovs:\n",
+    "    neighborhood_mask = load_utils.load_imgs_from_dir(\n",
+    "        data_dir=overlay_out_dir,\n",
+    "        files=[fov + \"_neighborhood_mask.tiff\"],\n",
+    "        trim_suffix=\"_neighborhood_mask\",\n",
+    "        match_substring=\"_neighborhood_mask\",\n",
+    "        xr_dim_name=\"neighborhood_mask\",\n",
+    "        xr_channel_names=None,\n",
+    "    )\n",
     "\n",
-    "plot_utils.plot_neighborhood_cluster_result(neighborhood_masks, fovs, k=k, save_dir=None)"
+    "    plot_utils.plot_neighborhood_cluster_result(neighborhood_mask, [fov], k=k, save_dir=None)"
    ]
   },
   {