Further testing of ATO based on imec, pnnl, rouen examples

atomprobe-tc · Nov 28, 2023 · c7edc5a · c7edc5a
1 parent cd641c9
commit c7edc5a
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Showing 4 changed files with 104 additions and 16 deletions.
diff --git a/ifes_apt_tc_data_modeling/ato/ato_reader.py b/ifes_apt_tc_data_modeling/ato/ato_reader.py
@@ -41,7 +41,8 @@ def __init__(self, filename: str):
         self.number_of_events = None
         self.version = None
         retval = self.get_ato_version()
-        if retval in [3, 4, 5]:
+        if retval in [3, 5]:
+            # there also seems to exist a version 4 but I have never seen an example for it
             self.version = retval
             print(f"ATO file is in a supported version {self.version}")
             if self.version == 3:
@@ -81,25 +82,26 @@ def get_reconstructed_positions(self):
         xyz.unit = "nm"
 
         if self.version == 3:
-            xyz.typed_value[:, 0] = \
-                get_memory_mapped_data(self.filename, "<f4",
-                                    2 * 4 + 0 * 4, 14 * 4, self.number_of_events)  # wpx -> x
-            xyz.typed_value[:, 1] = \
-                get_memory_mapped_data(self.filename, "<f4",
-                                    2 * 4 + 1 * 4, 14 * 4, self.number_of_events)  # wpy -> y
-            xyz.typed_value[:, 2] = \
-                get_memory_mapped_data(self.filename, "<f4",
-                                    2 * 4 + 2 * 4, 14 * 4, self.number_of_events)  # fpz -> z
+            for dim in [0, 1, 2]:
+                xyz.typed_value[:, dim] = \
+                    get_memory_mapped_data(self.filename, "<f4",
+                        2 * 4 + dim * 4, 14 * 4, self.number_of_events)
+                # wpx -> x, wpy -> y, fpz -> z
         if self.version == 5:
+            # publicly available sources are inconclusive whether coordinates are in angstroem or nm
+            # based on the evidence of usa_denton_smith Si.epos converted to v5 ATO via CamecaRoot
+            # the resulting x, y coordinates suggests that v5 ATO stores in angstroem, while fpz is stored in nm?
+            # however https://zenodo.org/records/8382828 reports the reconstructed positions to be named
+            # not at all wpx, wpy and fpz but x, y, z instead and here claims the nm
             xyz.typed_value[:, 0] = \
                 np.float32(get_memory_mapped_data(self.filename, "<i2",
-                                    5000 + 0, 40, self.number_of_events))  # wpx -> x
+                           5000 + 0, 40, self.number_of_events) * 0.1)  # wpx -> x
             xyz.typed_value[:, 1] = \
                 np.float32(get_memory_mapped_data(self.filename, "<i2",
-                                    5000 + 2, 40, self.number_of_events))  # wpy -> y
+                           5000 + 2, 40, self.number_of_events) * 0.1)  # wpy -> y
             xyz.typed_value[:, 2] = \
                 get_memory_mapped_data(self.filename, "<f4",
-                                    5000 + 4, 40, self.number_of_events)  # fpz -> z
+                                       5000 + 4, 40, self.number_of_events)  # fpz -> z
         return xyz
 
     def get_mass_to_charge_state_ratio(self):

diff --git a/ifes_apt_tc_data_modeling/rng/rng_reader.py b/ifes_apt_tc_data_modeling/rng/rng_reader.py
@@ -34,6 +34,9 @@
 
 from ase.data import atomic_numbers, atomic_masses, chemical_symbols
 
+# there are specific examples for unusual range files here:
+# https://hg.sr.ht/~mycae/libatomprobe/browse/test/samples/ranges?rev=tip
+
 
 def evaluate_rng_range_line(
         i: int, line: str, column_id_to_label: dict, n_columns: int) -> dict:

diff --git a/ifes_apt_tc_data_modeling/utils/dev/ato/ato.m b/ifes_apt_tc_data_modeling/utils/dev/ato/ato.m
@@ -0,0 +1,11 @@
+raw = fopen(["/home/kaiobach/Research/paper_paper_paper/joss_nomad_apt/bb_analysis/data/fra_rouen_karam/Experimental Analysis of LaB6 ; Negative Pulse ; DC Voltage 6.6 kV ; Amplitudes 2.5 kV and 3 kV.ato"]);
+attoread = inf; %max number of atoms
+data.version = fread(raw,2,'uint32','l');
+display(data.version(2));
+header = 5000;
+oneat = 320;
+fseek(raw,header,'bof');
+wpx = fread(raw,attoread,'int16',oneat/8-2,'b');
+fseek(raw,header+2,'bof');
+wpy = fread(raw,attoread,'int16',oneat/8-2,'b');
+fclose(raw);
diff --git a/tests/TestsForDevelopers.ipynb b/tests/TestsForDevelopers.ipynb
@@ -41,6 +41,80 @@
     "from ase.data import atomic_numbers, atomic_masses, chemical_symbols"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "52294143-78c7-47bf-b39e-9e40eec3999d",
+   "metadata": {},
+   "source": [
+    "## ATO"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f1c42976-c225-40f4-9797-bfcc0d566012",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from ifes_apt_tc_data_modeling.ato.ato_reader import ReadAtoFileFormat"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0d1f9d2f-ca12-4d74-9664-08a722d24c46",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "prefix = f\"{os.getcwd()}/../../../../../paper_paper_paper/joss_nomad_apt/bb_analysis/data\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "084d2bb0-5a52-49fa-af88-d9851db48521",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "directory = f\"{prefix}/usa_cameca_ato_format\"\n",
+    "fnm = [\"Si.epos.v3.ATO\",\n",
+    "       \"Si.epos.v5.ATO\"]\n",
+    "# directory = f\"{prefix}/bel_leuven_imec/dataverse_files/correlative-APT-EM\"\n",
+    "# fnm = [\"finfet/finfet_system.ato\",\n",
+    "#        \"multilayer/multilayer_system.ato\"]\n",
+    "# directory = f\"{prefix}/fra_rouen_karam\"\n",
+    "# fnm = [\"Experimental Analysis of LaB6 ; Negative Pulse ; DC Voltage 6.6 kV ; Amplitudes 2.5 kV and 3 kV.ato\",\n",
+    "#        \"Experimental Analysis of LaB6 ; Positive Pulse ; Amplitude 15 kV ; DC Voltage 3.2 kV and 5 kV.ato\",\n",
+    "#        \"Experimental Analysis of LaB6 ; Positive Pulse ; DC Voltage 2.5 kV ; Amplirudes 13.5 kV and 15 kV.ato\",\n",
+    "#        \"Experimental Analysis of LaB6 ; Positive Pulse ; DC Voltage 7 kV ; Amplitudes 6.5 kV and 7.5 kV.ato\"]\n",
+    "# directory = f\"{prefix}/usa_richland_kruska/kruska/APT\"\n",
+    "# fnm = [\"R31_11378-v01.ato\",\n",
+    "#        \"R31_11381-v02.ato\",\n",
+    "#        \"R31_11553-v01.ato\",\n",
+    "#        \"R31_11554-v01.ato\",\n",
+    "#        \"R31_11556-v01.ato\"]\n",
+    "print(directory)\n",
+    "for filename in fnm:\n",
+    "    print(os.path.getsize(f\"{directory}/{filename}\"))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b2a4eb3b-0a08-47a6-913b-cf4178e6bb24",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for filename in fnm:\n",
+    "    print(f\"{directory}/{filename}\")\n",
+    "    ato = ReadAtoFileFormat(f\"{directory}/{filename}\")\n",
+    "    \n",
+    "    xyz = ato.get_reconstructed_positions()\n",
+    "    print(xyz.typed_value)\n",
+    "    m_q = ato.get_mass_to_charge_state_ratio()\n",
+    "    print(m_q.typed_value)"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "83369dab-5ce9-4c9e-810e-58e9f8bb93cc",
@@ -415,7 +489,6 @@
    "cell_type": "markdown",
    "id": "0ab488b6-ddb3-4507-8f4e-de1c425106d6",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
    "source": [
@@ -527,7 +600,6 @@
    "cell_type": "markdown",
    "id": "8783c551-27b2-4902-93c4-2187b1ba0fab",
    "metadata": {
-    "jp-MarkdownHeadingCollapsed": true,
     "tags": []
    },
    "source": [
@@ -703,7 +775,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.16"
+   "version": "3.11.5"
   }
  },
  "nbformat": 4,