TIFF format

docs/supported_formats/tiff.rst

@@ -1,6 +1,6 @@
 .. _tiff-format:
 
-Tagges image file format (TIFF)
+Tagged image file format (TIFF)
 -------------------------------
 
 RosettaSciIO can read and write 2D and 3D ``.tiff`` files using using
@@ -23,6 +23,12 @@ RosettaSciIO can also import the scale and the units from ``.tiff`` files saved
 FEI, Zeiss SEM, Olympus SIS, Jeol SightX and Hamamatsu HPD-TA (streak camera)
 software.
 
+API functions
+^^^^^^^^^^^^^
+
+.. automodule:: rsciio.blockfile
+   :members:
+
 Extra loading arguments
 ^^^^^^^^^^^^^^^^^^^^^^^
 

rsciio/__init__.py

@@ -31,7 +31,7 @@
         with open(_specsf, "r") as stream:
             _specs = yaml.safe_load(stream)
             # for testing purposes
-            if _specs["name"] in ["Blockfile", "BrukerComposite", "Semper"]:
+            if _specs["name"] in ["Blockfile", "BrukerComposite", "Semper", "TIFF"]:
                 _specs["api"] = "rsciio.%s" % os.path.split(sub)[1]
             else:
                 _specs["api"] = "rsciio.%s.api" % os.path.split(sub)[1]

rsciio/tests/test_import.py

@@ -103,8 +103,18 @@ def test_dir_plugins():
 
     assert dir(bruker) == ["file_reader"]
 
-    # skimage is optional dependencies
+    # skimage is an optional dependency
     pytest.importorskip("skimage")
     from rsciio import blockfile
 
     assert dir(blockfile) == ["file_reader", "file_writer"]
+
+    from rsciio import semper_unf
+
+    assert dir(semper_unf) == ["file_reader", "file_writer"]
+
+    # tifffile is an optional dependency
+    pytest.importorskip("tifffile")
+    from rsciio import tiff
+
+    assert dir(tiff) == ["file_reader", "file_writer"]

rsciio/tests/test_tiff.py

@@ -28,7 +28,7 @@
 import pytest
 
 tifffile = pytest.importorskip("tifffile", reason="tifffile not installed")
-hs = pytest.importorskip("hyperspy.api", reason="hyperspy not installed")
+hs = pytest.importorskip("hyperspy._api", reason="hyperspy not installed")
 
 import traits.api as t
 
@@ -414,7 +414,7 @@ def test_saving_loading_stack_no_scale():
             "0": {
                 "operation": "load",
                 "hyperspy_version": hs.__version__,
-                "io_plugin": "rsciio.tiff.api",
+                "io_plugin": "rsciio.tiff._api",
             }
         },
     },
@@ -444,7 +444,7 @@ def test_saving_loading_stack_no_scale():
         "date": "2022-05-17",
         "time": "09:07:08",
         "authors": "user",
-        "FileIO": {"0": {"operation": "load", "io_plugin": "rsciio.tiff.api"}},
+        "FileIO": {"0": {"operation": "load", "io_plugin": "rsciio.tiff._api"}},
     },
     "Signal": {"signal_type": ""},
     "Acquisition_instrument": {
@@ -589,7 +589,7 @@ def test_read_Zeiss_SEM_scale_metadata_1k_image(self):
                     "0": {
                         "operation": "load",
                         "hyperspy_version": hs.__version__,
-                        "io_plugin": "rsciio.tiff.api",
+                        "io_plugin": "rsciio.tiff._api",
                     }
                 },
             },
@@ -643,7 +643,7 @@ def test_read_Zeiss_SEM_scale_metadata_512_image(self):
                     "0": {
                         "operation": "load",
                         "hyperspy_version": hs.__version__,
-                        "io_plugin": "rsciio.tiff.api",
+                        "io_plugin": "rsciio.tiff._api",
                     }
                 },
             },
@@ -685,7 +685,7 @@ def test_read_RGB_Zeiss_optical_scale_metadata():
     assert s.metadata.General.date == "2016-06-13"
     assert s.metadata.General.time == "15:59:52"
     assert s.metadata.General.FileIO.Number_0.hyperspy_version == hs.__version__
-    assert s.metadata.General.FileIO.Number_0.io_plugin == "rsciio.tiff.api"
+    assert s.metadata.General.FileIO.Number_0.io_plugin == "rsciio.tiff._api"
 
 
 def test_read_BW_Zeiss_optical_scale_metadata():
@@ -762,7 +762,7 @@ def test_read_TVIPS_metadata():
                 "0": {
                     "operation": "load",
                     "hyperspy_version": hs.__version__,
-                    "io_plugin": "rsciio.tiff.api",
+                    "io_plugin": "rsciio.tiff._api",
                 }
             },
         },
@@ -982,22 +982,22 @@ def test_is_hamamatsu_streak(self):
 
         omd["Artist"] = "TAPTAP"
 
-        assert not rsciio.tiff.api._is_streak_hamamatsu(omd)
+        assert not rsciio.tiff._api._is_streak_hamamatsu(omd)
 
         _ = omd.pop("Artist")
 
-        assert not rsciio.tiff.api._is_streak_hamamatsu(omd)
+        assert not rsciio.tiff._api._is_streak_hamamatsu(omd)
 
         omd.update({"Artist": "Copyright Hamamatsu GmbH, 2018"})
 
         omd["Software"] = "TAPTAPTAP"
 
-        assert not rsciio.tiff.api._is_streak_hamamatsu(omd)
+        assert not rsciio.tiff._api._is_streak_hamamatsu(omd)
 
         _ = omd.pop("Software")
 
-        assert not rsciio.tiff.api._is_streak_hamamatsu(omd)
+        assert not rsciio.tiff._api._is_streak_hamamatsu(omd)
 
         omd.update({"Software": "HPD-TA 9.5 pf4"})
 
-        assert rsciio.tiff.api._is_streak_hamamatsu(omd)
+        assert rsciio.tiff._api._is_streak_hamamatsu(omd)

rsciio/tiff/__init__.py

@@ -0,0 +1,11 @@
+from ._api import file_reader, file_writer
+
+
+__all__ = [
+    "file_reader",
+    "file_writer",
+]
+
+
+def __dir__():
+    return sorted(__all__)

rsciio/tiff/api.py → rsciio/tiff/_api.py

@@ -58,16 +58,21 @@
 
 
 def file_writer(filename, signal, export_scale=True, extratags=[], **kwds):
-    """Writes data to tif using Christoph Gohlke's tifffile library
+    """Writes data to tif using Christoph Gohlke's tifffile library.
 
     Parameters
     ----------
     filename: str
-    signal: a BaseSignal instance
-    export_scale: bool
-        default: True
+        Filename of the file to write to.
+    signal: dict
+        Dictionary containing the signal object as defined in the `API guide
+        <https://hyperspy.org/rosettasciio/api.html>`_.
+    export_scale: bool, default=True
         Export the scale and the units (compatible with DM and ImageJ) to
         appropriate tags.
+    **kwds, optional
+        Additional arguments to be passed to the `tifffile library
+        <https://github.com/cgohlke/tifffile/#examples>`_
     """
 
     data = signal["data"]
@@ -103,7 +108,7 @@ def file_writer(filename, signal, export_scale=True, extratags=[], **kwds):
     imwrite(filename, data, software="hyperspy", photometric=photometric, **kwds)
 
 
-def file_reader(filename, force_read_resolution=False, lazy=False, **kwds):
+def file_reader(filename, lazy=False, force_read_resolution=False, **kwds):
     """
     Read data from tif files using Christoph Gohlke's tifffile library.
     The units and the scale of images saved with ImageJ or Digital
@@ -113,15 +118,16 @@ def file_reader(filename, force_read_resolution=False, lazy=False, **kwds):
     Parameters
     ----------
     filename: str
-        Name of the file to read
-    force_read_resolution: bool
+        Name of the file to read.
+    lazy : bool, Default=False
+        Load the data lazily.
+    force_read_resolution: bool, Default=False
         Force reading the x_resolution, y_resolution and the resolution_unit
         of the tiff tags.
-        See https://www.awaresystems.be/imaging/tiff/tifftags/resolutionunit.html
-        Default is False.
-    lazy : bool
-        Load the data lazily. Default is False
+        See `<https://www.awaresystems.be/imaging/tiff/tifftags/resolutionunit.html>`_
     **kwds, optional
+        Additional arguments to be passed to the `tifffile library
+        <https://github.com/cgohlke/tifffile/#examples>`_
     """
     tmp = kwds.pop("hamamatsu_streak_axis_type", None)