From 020dea06adb64cd3124b84bee55c938437f0f104 Mon Sep 17 00:00:00 2001
From: mkuehbach <markus.kuehbach@physik.hu-berlin.de>
Date: Fri, 8 Dec 2023 17:09:29 +0100
Subject: [PATCH] Added working skeleton code for the TFS-specific TIFF parser,
 which fishes successfully metadata and converts into standardized python
 dict, ods document added to collect IKZ feedback how to map specific TFS
 using assumptions onto specific concepts in NXem to consume in e.g. OASIS

---
 image_tiff_tfs_to_nexus.ods                   | Bin 0 -> 17720 bytes
 imgs.batch.sh                                 |   2 +-
 imgs.dev.ipynb                                |   7 +-
 .../readers/em/subparsers/image_tiff_tfs.py   | 130 ++++++++++++++++++
 .../em/subparsers/image_tiff_tfs_cfg.py       |  62 +++++++++
 .../readers/em/subparsers/nxs_imgs.py         |  10 +-
 .../readers/em/utils/image_utils.py           |  40 ++++++
 7 files changed, 243 insertions(+), 8 deletions(-)
 create mode 100644 image_tiff_tfs_to_nexus.ods
 create mode 100644 pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py
 create mode 100644 pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs_cfg.py
 create mode 100644 pynxtools/dataconverter/readers/em/utils/image_utils.py

diff --git a/image_tiff_tfs_to_nexus.ods b/image_tiff_tfs_to_nexus.ods
new file mode 100644
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HcmV?d00001

diff --git a/imgs.batch.sh b/imgs.batch.sh
index 90a0cf7cf..a764c63d4 100755
--- a/imgs.batch.sh
+++ b/imgs.batch.sh
@@ -2,7 +2,7 @@
 
 datasource="../../../../paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/production_imgs/"
 
-examples="ALN_baoh_021.tif FeMoOx_AntiA_04_1k5x_CN.tif"
+examples="ALN_baoh_021.tif"  # FeMoOx_AntiA_04_1k5x_CN.tif"
 
 for example in $examples; do
 	echo $example
diff --git a/imgs.dev.ipynb b/imgs.dev.ipynb
index deee2d480..82317d0a6 100755
--- a/imgs.dev.ipynb
+++ b/imgs.dev.ipynb
@@ -8,7 +8,7 @@
    "outputs": [],
    "source": [
     "fnm = \"/home/kaiobach/Research/paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/production_imgs/ALN_baoh_021.tif\"\n",
-    "fnm = \"/home/kaiobach/Research/paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/production_imgs/FeMoOx_AntiA_04_1k5x_CN.tif\""
+    "# fnm = \"/home/kaiobach/Research/paper_paper_paper/scidat_nomad_ebsd/bb_analysis/data/production_imgs/FeMoOx_AntiA_04_1k5x_CN.tif\""
    ]
   },
   {
@@ -18,6 +18,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import numpy as np\n",
     "from PIL import Image\n",
     "from PIL.TiffTags import TAGS\n",
     "# print(TAGS)"
@@ -58,14 +59,16 @@
     "    czi_keys = [34118, 34119]\n",
     "    for czi_key in czi_keys:\n",
     "        if czi_key in fp.tag_v2:\n",
+    "            print(f\"Found czi_key {tfs_key}...\")\n",
     "            utf = fp.tag[czi_key]\n",
     "            print(type(utf))\n",
     "            if len(utf) == 1:\n",
     "                print(utf[0])\n",
-    "    exit(1)\n",
+    "    # exit(1)\n",
     "    tfs_keys = [34682]\n",
     "    for tfs_key in tfs_keys:\n",
     "        if tfs_key in fp.tag_v2:\n",
+    "            print(f\"Found tfs_key {tfs_key}...\")\n",
     "            utf = fp.tag[tfs_key]\n",
     "            print(type(utf))\n",
     "            if len(utf) == 1:\n",
diff --git a/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py b/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py
new file mode 100644
index 000000000..6fbd61fba
--- /dev/null
+++ b/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs.py
@@ -0,0 +1,130 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""Subparser for harmonizing ThermoFisher-specific content in TIFF files."""
+
+import mmap
+import numpy as np
+from typing import Dict
+from PIL import Image
+from PIL.TiffTags import TAGS
+
+from pynxtools.dataconverter.readers.em.subparsers.image_tiff import TiffSubParser
+from pynxtools.dataconverter.readers.em.subparsers.image_tiff_tfs_cfg import \
+    tfs_section_names, tfs_section_details
+from pynxtools.dataconverter.readers.em.utils.image_utils import \
+    sort_tuple, if_str_represents_float
+
+
+class TfsTiffSubParser(TiffSubParser):
+    def __init__(self, file_path: str = ""):
+        super().__init__(file_path)
+        self.prfx = None
+        self.tmp: Dict = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
+        self.tags: Dict = {}
+        self.supported = False
+        self.check_if_tiff()
+        self.tfs: Dict = {}
+
+    def check_if_tiff_tfs(self):
+        """Check if resource behind self.file_path is a TaggedImageFormat file."""
+        self.supported = 0  # voting-based
+        with open(self.file_path, 'rb', 0) as file:
+            s = mmap.mmap(file.fileno(), 0, access=mmap.ACCESS_READ)
+            magic = s.read(4)
+            if magic == b'II*\x00':  # https://en.wikipedia.org/wiki/TIFF
+                self.supported += 1
+
+        with Image.open(self.fiele_path, mode="r") as fp:
+            tfs_keys = [34682]
+            for tfs_key in tfs_keys:
+                if tfs_key in fp.tag_v2:
+                    if len(fp.tag[tfs_key]) == 1:
+                        self.supported += 1  # found TFS-specific tag
+        if self.supported == 2:
+            self.supported = True
+        else:
+            self.supported = False
+
+    def get_metadata(self):
+        """Extract metadata in TFS specific tags if present."""
+        print("Reporting the tags found in this TIFF file...")
+        # for an overview of tags
+        # https://www.loc.gov/preservation/digital/formats/content/tiff_tags.shtml
+        # with Image.open(self.file_path, mode="r") as fp:
+        #     self.tags = {TAGS[key] : fp.tag[key] for key in fp.tag_v2}
+        #     for key, val in self.tags.items():
+        #         print(f"{key}, {val}")
+        tfs_section_offsets = {}
+        with open(self.file_path, 'rb', 0) as fp:
+            s = mmap.mmap(fp.fileno(), 0, access=mmap.ACCESS_READ)
+            for section_name in tfs_section_names:
+                pos = s.find(bytes(section_name, "utf8"))  # != -1
+                tfs_section_offsets[section_name] = pos
+            print(tfs_section_offsets)
+
+            # define search offsets
+            tpl = []
+            for key, value in tfs_section_offsets.items():
+                tpl.append((key, value))
+            tpl = sort_tuple(tpl)
+            print(tpl)
+
+            # exemplar parsing of specific TFS section content into a dict
+            # here for section_name == "[System]":
+            pos_s = None
+            pos_e = None
+            for idx in np.arange(0, len(tpl)):
+                if tpl[idx][0] != "[System]":
+                    continue
+                else:
+                    pos_s = tpl[idx][1]
+                    if idx <= len(tpl) - 1:
+                        pos_e = tpl[idx + 1][1]
+                    break
+            print(f"Search for [System] in between byte offsets {pos_s} and {pos_e}")
+            if pos_s is None or pos_e is None:
+                raise ValueError(f"Search for [System] was unsuccessful !")
+
+            # fish metadata of e.g. the system section
+            for term in tfs_section_details["[System]"]:
+                s.seek(pos_s, 0)
+                pos = s.find(bytes(term, "utf8"))
+                if pos < pos_e:  # check if pos_e is None
+                    s.seek(pos, 0)
+                    value = f"{s.readline().strip().decode('utf8').replace(f'{term}=', '')}"
+                    if value != "":
+                        if if_str_represents_float(value) is True:
+                            self.tfs[f"system/{term}"] = np.float64(value)
+                        elif value.isdigit() is True:
+                            self.tfs[f"system/{term}"] = np.int64(value)
+                        else:
+                            self.tfs[f"system/{term}"] = None
+                else:
+                    pass
+            print(self.tfs)
+
+    def parse_and_normalize(self):
+        """Perform actual parsing filling cache self.tmp."""
+        if self.supported is True:
+            print(f"Parsing via ThermoFisher-specific metadata...")
+            self.get_metadata()
+        else:
+            print(f"{self.file_path} is not a ThermoFisher-specific "
+                  f"TIFF file that this parser can process !")
diff --git a/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs_cfg.py b/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs_cfg.py
new file mode 100644
index 000000000..53797ce87
--- /dev/null
+++ b/pynxtools/dataconverter/readers/em/subparsers/image_tiff_tfs_cfg.py
@@ -0,0 +1,62 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+"""Configuration of the image_tiff_tfs subparser."""
+
+
+tfs_section_names = ["[User]",
+                     "[System]",
+                     "[Beam]",
+                     "[EBeam]",
+                     "[GIS]",
+                     "[Scan]",
+                     "[EScan]",
+                     "[Stage]",
+                     "[Image]",
+                     "[Vacuum]",
+                     "[Specimen]",
+                     "[Detectors]",
+                     "[T2]",
+                     "[Accessories]",
+                     "[EBeamDeceleration]",
+                     "[CompoundLensFilter]",
+                     "[PrivateFei]",
+                     "[HiResIllumination]",
+                     "[EasyLift]",
+                     "[HotStageMEMS]",
+                     "[HotStage]",
+                     "[HotStageHVHS]",
+                     "[ColdStage]"]
+
+tfs_section_details = {"[System]": ["Type",
+                                    "Dnumber",
+                                    "Software",
+                                    "BuildNr",
+                                    "Source",
+                                    "Column",
+                                    "FinalLens",
+                                    "Chamber",
+                                    "Stage",
+                                    "Pump",
+                                    "ESEM",
+                                    "Aperture",
+                                    "Scan",
+                                    "Acq",
+                                    "EucWD",
+                                    "SystemType",
+                                    "DisplayWidth",
+                                    "DisplayHeight"]}
diff --git a/pynxtools/dataconverter/readers/em/subparsers/nxs_imgs.py b/pynxtools/dataconverter/readers/em/subparsers/nxs_imgs.py
index 6b2c2f479..495cec07b 100644
--- a/pynxtools/dataconverter/readers/em/subparsers/nxs_imgs.py
+++ b/pynxtools/dataconverter/readers/em/subparsers/nxs_imgs.py
@@ -20,7 +20,7 @@
 import numpy as np
 # from typing import Dict, Any, List
 
-from pynxtools.dataconverter.readers.em.subparsers.image_tiff import TiffSubParser
+from pynxtools.dataconverter.readers.em.subparsers.image_tiff_tfs import TfsTiffSubParser
 
 
 class NxEmImagesSubParser:
@@ -38,9 +38,9 @@ def __init__(self, entry_id: int = 1, input_file_name: str = ""):
     def identify_image_type(self):
         """Identify if image matches known mime type and has content for which subparser exists."""
         # tech partner formats used for measurement
-        img = TiffSubParser(f"{self.file_path}")
+        img = TfsTiffSubParser(f"{self.file_path}")
         if img.supported is True:
-            return "tiff"
+            return "tiff_tfs"
         return None
 
     def parse(self, template: dict) -> dict:
@@ -52,8 +52,8 @@ def parse(self, template: dict) -> dict:
         # see also comments for respective nxs_pyxem parser
         # and its interaction with tech-partner-specific hfive_* subparsers
 
-        if image_parser_type == "tiff":
-            tiff = TiffSubParser(self.file_path)
+        if image_parser_type == "tiff_tfs":
+            tiff = TfsTiffSubParser(self.file_path)
             tiff.parse_and_normalize()
             self.process_into_template(tiff.tmp, template)
         else:  # none or something unsupported
diff --git a/pynxtools/dataconverter/readers/em/utils/image_utils.py b/pynxtools/dataconverter/readers/em/utils/image_utils.py
new file mode 100644
index 000000000..342af0bfc
--- /dev/null
+++ b/pynxtools/dataconverter/readers/em/utils/image_utils.py
@@ -0,0 +1,40 @@
+#
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+import numpy as np
+
+
+# https://www.geeksforgeeks.org/python-program-to-sort-a-list-of-tuples-by-second-item/
+def sort_tuple(tup):
+    # convert the list of tuples to a numpy array with data type (object, int)
+    arr = np.array(tup, dtype=[('col1', object), ('col2', int)])
+    # get the indices that would sort the array based on the second column
+    indices = np.argsort(arr['col2'])
+    # use the resulting indices to sort the array
+    sorted_arr = arr[indices]
+    # convert the sorted numpy array back to a list of tuples
+    sorted_tup = [(row['col1'], row['col2']) for row in sorted_arr]
+    return sorted_tup
+
+
+def if_str_represents_float(s):
+    try:
+        float(s)
+        return str(float(s)) == s
+    except ValueError:
+        return False