Update documentation to reflect manual copying of directory structure

templates/maldi-pipeline.ipynb

@@ -50,15 +50,13 @@
     "\n",
     "### 1.1. File paths\n",
     "\n",
-    "The following variables are defined pointing to paths in your MALDI run.\n",
+    "The following variables are defined pointing to paths in your MALDI run. **Only `base_dir` should be changed, the other folders should maintain the existing names and subdirectory structure.**\n",
     "\n",
-    "* `base_dir`: the path to your MALDI data. **Change this to match your run location**.\n",
-    "* `library_dir`: the path inside `base_dir` to your `\"libraries\"` folder. This will contain the master list to use for glycan matching.\n",
-    "* `extraction_dir`: the path inside `base_dir` to your `\"extracted\"` folder. Contains the integrated images for each filtered peak and glycan-matched peak across the slide.\n",
-    "* `debug_dir`: the path inside `base_dir` to your `\"debug\"` folder. Individual peak height and width info is saved here for debugging purposes.\n",
-    "* `imzml_dir`: the path inside `base_dir` to your `\"imzml\"` folder. This will contain the `\".imzml\"` and `\".ibd\"` files extracted from SCiLS.\n",
-    "* `imzml_file`: the name of the `imzml` file saved inside the `imzml_dir`. **Change this to match your imzml file name**.\n",
-    "* `imzml_path`: the full path to the `imzml_file`"
+    "* `base_dir`: the path to your MALDI data.\n",
+    "* `imzml_dir`: the path inside `base_dir` to your `imzml` folder. This will contain the `.imzml` and `.ibd` files extracted from SCiLS.\n",
+    "* `library_dir`: the path inside `base_dir` to your `libraries` folder. This will contain the master list to use for glycan matching.\n",
+    "* `extraction_dir`: the path inside `base_dir` to your `extracted` folder. Contains the integrated images for each filtered peak and glycan-matched peak across the slide.\n",
+    "* `debug_dir`: the path inside `base_dir` to your `debug` folder. Individual peak height and width info is saved here for debugging purposes."
    ]
   },
   {
@@ -70,13 +68,10 @@
    "outputs": [],
    "source": [
     "base_dir = pathlib.Path(\"../data/panc2055\")\n",
-    "library_dir = base_dir / \"libraries\"\n",
-    "extraction_dir = base_dir / data_name / \"extracted\"\n",
-    "debug_dir = base_dir / data_name / \"debug\"\n",
-    "\n",
     "imzml_dir = base_dir / \"imzml\"\n",
-    "imzml_file = \"panc2055.imzML\"\n",
-    "imzml_path = imzml_dir / data_file"
+    "library_dir = base_dir / \"libraries\"\n",
+    "extraction_dir = base_dir / \"output\" / \"extracted\"\n",
+    "debug_dir = base_dir / \"output\" / \"debug\""
    ]
   },
   {
@@ -95,11 +90,35 @@
    "outputs": [],
    "source": [
     "# Create directories\n",
-    "for directory in [base_dir, library_dir, extraction_dir, debug_dir]:\n",
+    "for directory in [base_dir, imzml_dir, library_dir, extraction_dir, debug_dir]:\n",
     "    if not os.path.exists(directory):\n",
     "        directory.mkdir(parents=True, exist_ok=True)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**NOTE: At this point, ensure you have the following files in your folders in the following locations:**\n",
+    "\n",
+    "* .imzml/.ibd files: extracted using SCiLS. **Either explicitly point to the `imzml` subfolder when extracting, or manually copy these files to the `imzml` subfolder afterwards.**\n",
+    "* Master glycan list: defining a singular master glycan list is a WIP. For now, ask a lab member for the peak list to use. **This file must be manually copied into the `\"libraries\"` subfolder.**\n",
+    "\n",
+    "And define the following variable:\n",
+    "\n",
+    "* `imzml_file`: the name of the `.imzml` file in the `imzml` subfolder."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "imzml_file = \"panc2055.imzml\"\n",
+    "imzml_path = imzml_file / imzml_path"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -170,7 +189,7 @@
    "outputs": [],
    "source": [
     "# define the .imzml/.ibd loader object\n",
-    "imz_data = ImzMLParser(data_path, include_spectra_metadata=\"full\")\n",
+    "imz_data = ImzMLParser(imzml_path, include_spectra_metadata=\"full\")\n",
     "\n",
     "# extract the spectra and threshold array\n",
     "total_mass_df, thresholds = extraction.extract_spectra(\n",
@@ -222,9 +241,7 @@
    "source": [
     "### 2.2. Master library peaks\n",
     "\n",
-    "Load the master glycan peak list, this will be used by the library matching process.\n",
-    "\n",
-    "**NOTE: Defining a singular master glycan peaklist is a WIP. For now, ask a lab member for the peak list to use. This file must be manually copied into the `\"libraries\"` subfolder.**"
+    "Load the master glycan peak list, this will be used by the library matching process."
    ]
   },
   {
@@ -661,7 +678,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.11.9"
   },
   "vscode": {
    "interpreter": {