Added functions to parse mesoSPIM metadata

.github/workflows/docs_build_and_deploy.yml

@@ -10,7 +10,7 @@ on:
     branches:
       - main
     tags:
-      - '*'
+      - 'v*'
   pull_request:
   workflow_dispatch:
 

LICENSE

@@ -12,7 +12,7 @@ modification, are permitted provided that the following conditions are met:
   this list of conditions and the following disclaimer in the documentation
   and/or other materials provided with the distribution.
 
-* Neither the name of mesoSPIM-stitcher nor the names of its
+* Neither the name of mesospim-stitcher nor the names of its
   contributors may be used to endorse or promote products derived from
   this software without specific prior written permission.
 

MANIFEST.in

@@ -2,6 +2,8 @@ include LICENSE
 include README.md
 exclude .pre-commit-config.yaml
 
+recursive-include mesospim_stitcher *.py
+
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 recursive-exclude docs *

README.md

@@ -1 +1 @@
-# mesoSPIM-stitcher
+# mesospim-stitcher

docs/source/api_index.rst

@@ -4,7 +4,7 @@ API
 math
 ----
 
-.. currentmodule:: mesoSPIM-stitcher.math
+.. currentmodule:: mesospim-stitcher.math
 
 .. autosummary::
     :toctree: api_generated
@@ -16,7 +16,7 @@ math
 greetings
 ---------
 
-.. currentmodule:: mesoSPIM-stitcher.greetings
+.. currentmodule:: mesospim-stitcher.greetings
 
 .. autosummary::
     :toctree: api_generated

docs/source/conf.py

@@ -20,7 +20,7 @@
 # use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath("../.."))
 
-project = "mesoSPIM-stitcher"
+project = "mesospim_stitcher"
 copyright = "2023, Igor Tatarnikov"
 author = "Igor Tatarnikov"
 try:
@@ -86,7 +86,7 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 html_theme = "pydata_sphinx_theme"
-html_title = "mesoSPIM-stitcher"
+html_title = "mesospim_stitcher"
 
 # Customize the theme
 html_theme_options = {

docs/source/index.rst

@@ -1,9 +1,9 @@
-.. mesoSPIM-stitcher documentation master file, created by
+.. mesospim-stitcher documentation master file, created by
    sphinx-quickstart on Fri Dec  9 14:12:42 2022.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-Welcome to mesoSPIM-stitcher's documentation!
+Welcome to mesospim-stitcher's documentation!
 =========================================================
 
 .. toctree::

mesoSPIM-stitcher/__init__.py → mesospim_stitcher/__init__.py

@@ -1,7 +1,7 @@
 from importlib.metadata import PackageNotFoundError, version
 
 try:
-    __version__ = version("mesoSPIM-stitcher")
+    __version__ = version("mesospim_stitcher")
 except PackageNotFoundError:
     # package is not installed
     pass

mesospim_stitcher/file_utils.py

@@ -0,0 +1,84 @@
+from pathlib import Path
+
+HEADERS = [
+    "[POSITION]",
+    "[ETL PARAMETERS]",
+    "[GALVO PARAMETERS]",
+    "[CAMERA PARAMETERS]",
+]
+
+
+def write_big_stitcher_tile_config(meta_file_name: Path) -> list[dict]:
+    tile_metadata = parse_mesospim_metadata(meta_file_name)
+
+    output_file = str(meta_file_name)[:-12] + "_tile_config.txt"
+
+    first_channel = tile_metadata[0]["Laser"]
+    num_channels = 1
+
+    for metadata in tile_metadata[1:]:
+        if metadata["Laser"] == first_channel:
+            break
+        else:
+            num_channels += 1
+
+    num_tiles = len(tile_metadata) // num_channels
+    tile_xy_locations = []
+
+    for i in range(0, len(tile_metadata), num_channels):
+        curr_tile_dict = tile_metadata[i]
+
+        x = round(curr_tile_dict["x_pos"] / curr_tile_dict["Pixelsize in um"])
+        y = round(curr_tile_dict["y_pos"] / curr_tile_dict["Pixelsize in um"])
+
+        tile_xy_locations.append((x, y))
+
+    relative_locations = [(0, 0)]
+
+    for abs_tuple in tile_xy_locations[1:]:
+        rel_tuple = (
+            abs(abs_tuple[0] - tile_xy_locations[0][0]),
+            abs(abs_tuple[1] - tile_xy_locations[0][1]),
+        )
+        relative_locations.append(rel_tuple)
+
+    with open(output_file, "w") as f:
+        f.write("dim=3\n")
+        for i in range(len(tile_metadata)):
+            f.write(
+                f"{i};;"
+                f"({relative_locations[i%num_tiles][0]},"
+                f"{relative_locations[i%num_tiles][1]},0)\n"
+            )
+
+    return tile_metadata
+
+
+def parse_mesospim_metadata(meta_file_name: Path):
+    tile_metadata = []
+    with open(meta_file_name, "r") as f:
+        lines = f.readlines()
+        curr_tile_metadata: dict[str, str | int | float] = {}
+
+        for line in lines[3:]:
+            line = line.strip()
+            if line.startswith("[CFG"):
+                tile_metadata.append(curr_tile_metadata)
+                curr_tile_metadata = {}
+            elif line in HEADERS:
+                continue
+            elif not line:
+                continue
+            else:
+                split_line = line.split("]")
+                value = split_line[1].strip()
+                if value.isdigit():
+                    curr_tile_metadata[split_line[0][1:]] = int(value)
+                else:
+                    try:
+                        curr_tile_metadata[split_line[0][1:]] = float(value)
+                    except ValueError:
+                        curr_tile_metadata[split_line[0][1:]] = value
+
+    tile_metadata.append(curr_tile_metadata)
+    return tile_metadata

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "mesoSPIM-stitcher"
+name = "mesospim-stitcher"
 authors = [{name = "Igor Tatarnikov", email= "[email protected]"}]
 description = "A tool to stich large tiled datasets generated by the mesoSPIM."
 readme = "README.md"
@@ -52,12 +52,12 @@ build-backend = "setuptools.build_meta"
 include-package-data = true
 
 [tool.setuptools.packages.find]
-include = ["mesoSPIM-stitcher*"]
+include = ["mesospim-stitcher*"]
 exclude = ["tests", "docs*"]
 
 
 [tool.pytest.ini_options]
-addopts = "--cov=mesoSPIM-stitcher"
+addopts = "--cov=mesospim-stitcher"
 
 [tool.black]
 target-version = ['py39', 'py310', 'py311']
@@ -100,5 +100,5 @@ python =
 extras =
     dev
 commands =
-    pytest -v --color=yes --cov=mesoSPIM-stitcher --cov-report=xml
+    pytest -v --color=yes --cov=mesospim-stitcher --cov-report=xml
 """