Change hands-on: from Fit2D to PONI

silx-kit · Apr 3, 2024 · 4ec378c · 4ec378c
1 parent 6d4f5af
commit 4ec378c
Showing 1 changed file with 65 additions and 52 deletions.
diff --git a/python/python/3_input_output.ipynb b/python/python/3_input_output.ipynb
@@ -337,27 +337,52 @@
    "source": [
     "## Hands on\n",
     "\n",
-    "Read an ascii spreadsheet written by FIT2D:\n",
+    "A scattering geometry can be entirely described with a Point of Normal Incidence (PONI).  \n",
+    "This is the coordinates of the orthogonal projection of center of sample onto the detector.\n",
     "\n",
-    "* The first non commented line looks like:\n",
-    "    * `512 512 Start pixel = ( 1 1 )`\n",
-    "    * Then 512 values per line, 512 lines\n",
-    "* Read the file as a list of lists and display as an image.\n",
     "\n",
-    "If `data` is a list of lists (of float), this can be done using matlab with:\n",
-    "\n",
-    "``` python\n",
-    "%matplotlib inline\n",
-    "from matplotlib.pyplot import subplots\n",
+    "![sd](img/PONI.png)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "slideshow": {
+     "slide_type": "slide"
+    }
+   },
+   "source": [
+    "[pyFAI](https://pyfai.readthedocs.io/en/latest/) uses a PONI file to describe the geometry.  \n",
+    "It looks like this:\n",
     "\n",
-    "fig, ax = subplots()\n",
-    "ax.imshow(data)\n",
+    "```yaml\n",
+    "poni_version: 2.1\n",
+    "Detector: Eiger2_4M\n",
+    "Detector_config: {\"orientation\": 3}\n",
+    "Distance: 0.41826947072547654\n",
+    "Poni1: 0.1273645012076586\n",
+    "Poni2: 0.04721622971911041\n",
+    "Rot1: -0.006558391003187438\n",
+    "Rot2: -0.001319758222137916\n",
+    "Rot3: 4.987612019731912e-06\n",
+    "Wavelength: 1.6531226457760035e-11\n",
     "```\n",
     "\n",
-    "* Example file in : data/example.spr\n",
-    "\n",
-    "\n",
-    "![FIT2D image saved in ASCII](img/fit2d_ascii_file.png \"FIT2D image saved in ASCII\")\n"
+    "**Exercise** read the above information from the file `data/eiger.poni`, and store it in a dictionary.  \n",
+    "It should look like:  \n",
+    "```python\n",
+    "{'poni_version': '2.1',\n",
+    " 'Detector': 'Eiger2_4M',\n",
+    " 'Detector_config': ' {\"orientation\" 3}',\n",
+    " 'Distance': '0.41826947072547654',\n",
+    " 'Poni1': '0.1273645012076586',\n",
+    " 'Poni2': '0.04721622971911041',\n",
+    " 'Rot1': '-0.006558391003187438',\n",
+    " 'Rot2': '-0.001319758222137916',\n",
+    " 'Rot3': '4.987612019731912e-06',\n",
+    " 'Wavelength': '1.6531226457760035e-11'\n",
+    "}\n",
+    "```"
    ]
   },
   {
@@ -381,38 +406,31 @@
    },
    "outputs": [],
    "source": [
-    "def readspr(filepath):\n",
-    "    \"Read a FIT2D ascii spread file\"\n",
-    "    result = []\n",
-    "    xsize = 0\n",
-    "    ysize = 0\n",
+    "def read_poni(filepath, comment=\"#\"):\n",
+    "    \"Read a PONI file\"\n",
+    "    poni_info = {}\n",
     "    with open(filepath, \"r\") as opened_file:\n",
-    "        for idx, line in enumerate(opened_file):\n",
-    "            strippedline = line.strip()\n",
-    "            # if this is a commented line\n",
-    "            if strippedline.startswith(\"#\"):\n",
+    "        for line in opened_file:\n",
+    "            # Sanitize current line: remove leading and trailing spaces\n",
+    "            line = line.strip()\n",
+    "            # Skip commented lines\n",
+    "            if line.startswith(comment):\n",
     "                continue\n",
-    "            words = strippedline.split()\n",
-    "            if (len(words) == 8) and (words[2:6] == [\"Start\", \"pixel\", \"=\", \"(\"]):\n",
-    "                xsize = int(words[0])\n",
-    "                ysize = int(words[1])\n",
-    "                print(\"Dimensions of the size are (%s, %s)\" % (xsize, ysize))\n",
-    "                break\n",
-    "        if xsize and ysize:\n",
-    "            for line in opened_file:\n",
-    "                words = line.split()\n",
-    "                if len(words) != xsize:\n",
-    "                    print(\n",
-    "                        \"Error !!! Expected entries are %s, got %s\"\n",
-    "                        % (xsize, len(words))\n",
-    "                    )\n",
-    "                    return None\n",
-    "                else:\n",
-    "                    result.append([float(i) for i in words])\n",
-    "    return result\n",
-    "\n",
-    "\n",
-    "data = readspr(\"data/example.spr\")"
+    "            # Split the line before and after the \":\" separator\n",
+    "            fields = line.split(\":\")\n",
+    "            name = fields[0]\n",
+    "            if len(fields) == 2:\n",
+    "                value = fields[1].strip()\n",
+    "            elif len(fields) > 2:\n",
+    "                value = \"\".join(fields[1:])\n",
+    "            else:\n",
+    "                continue\n",
+    "                value = value.strip()\n",
+    "            poni_info[name] = value\n",
+    "    return poni_info\n",
+    "\n",
+    "\n",
+    "data = read_poni(\"data/eiger.poni\")"
    ]
   },
   {
@@ -425,12 +443,7 @@
    },
    "outputs": [],
    "source": [
-    "# Display the image\n",
-    "%matplotlib inline\n",
-    "from matplotlib.pyplot import subplots\n",
-    "\n",
-    "fig, ax = subplots()\n",
-    "ax.imshow(data)"
+    "data"
    ]
   },
   {