Merge pull request #80 from mobie/fix-trafos

Extend transformation functionality

examples/create_mobie_project.ipynb

@@ -97,7 +97,8 @@
     "#           good choices are usually (1, 512, 512) for 2d data and (64, 64, 64) for 3d data\n",
     "# - scale_factors: the scale factors used for downsampling the input when creating the image pyramid\n",
     "#                  this needs to be a list, where each entry specifies the scale factors for the 3 axes.\n",
-    "# Note that axes are always listed in the order ZYX here (in the java implementation of mobie / big-data-viewer the axis convention is XYZ).\n",
+    "# Note that axes are listed in the order ZYX for the resolution, chunks and scale factors\n",
+    "# (in the java implementation of mobie / big-data-viewer the axis convention is XYZ).\n",
     "# Also note that the values for all three axes (ZYX) need to be specified. In the case of 2d data, the value\n",
     "# for Z should be set to 1.\n",
     "unit = \"nanometer\"\n",
@@ -157,6 +158,8 @@
     "# the 2d em overview. This is achieved via an affine transformation,\n",
     "# that has been determined externally and will be applied on the fly by big-data-viewer.\n",
     "# Each affine transformation contains 12 parameters.\n",
+    "# Note that the transformations here have to be specified in the 'native' axis order for bdv/mobie\n",
+    "# this means they are given in XYZ order, unlike the other parameters that are given in ZYX\n",
     "transformations = [\n",
     "    [5.098000335693359, 0.0, 0.0, 54413.567834472655,\n",
     "     0.0, 5.098000335693359, 0.0, 51514.319843292236,\n",
@@ -166,6 +169,22 @@
     "     0.0, 0.0, 5.098000335693359, 0.0]\n",
     "]\n",
     "\n",
+    "# if you have transformations that were determined with some tool in python, they are usually given in the ZYX order.\n",
+    "# you can use the following code to translate them to the correct XYZ order:\n",
+    "\n",
+    "# # assume 'trafo' is a transformation in zyx axis order:\n",
+    "# from mobie.utils import transformation_to_xyz\n",
+    "# trafo = transformation_to_xyz(trafo)\n",
+    "\n",
+    "# it might also be necessary to change the transformation order\n",
+    "# (this is because some tools specify transformations in forward order, some in backward order)\n",
+    "# in this case use\n",
+    "# trafo = transformation_to_xyz(trafo, invert=True)\n",
+    "\n",
+    "# (in practice you probably need to figure this out with trial and error)\n",
+    "# (sorry if this is confusing, but automatically changing this for the transformations can lead to \n",
+    "# a lot of subtle errors, so I decided against doing this)\n",
+    "\n",
     "# add the two tomograms\n",
     "for name, trafo in zip(tomo_names, transformations):\n",
     "    im_name = os.path.splitext(name)[0]\n",

mobie/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.3.0"
+__version__ = "0.3.2"
 SPEC_VERSION = "0.2.0"

mobie/utils.py

@@ -4,6 +4,7 @@
 import os
 from copy import deepcopy
 
+import elf.transformation as trafo_helper
 import mobie.metadata as metadata
 from cluster_tools.cluster_tasks import BaseClusterTask
 from elf.io import open_file
@@ -246,3 +247,17 @@ def write_global_config(config_folder,
 
     with open(conf_path, "w") as f:
         json.dump(global_config, f)
+
+
+def transformation_to_xyz(transform, invert=False):
+    """Convert a transformation from zyx coordinates (python default)
+    to xyz coordinates (expected by mobie).
+
+    Arguments:
+        transform [list, np.ndarray] - the transformation parameters (12 values = upper 3 rows of affine matrix)
+        invert [bool] - whether to invert the transformation.
+            This can be necessary because e.g. scipy uses the different transformation direction (default: False)
+    """
+    trafo = trafo_helper.parameters_to_matrix(transform)
+    trafo = trafo_helper.native_to_bdv(trafo, invert=invert)
+    return trafo

mobie/xml_utils.py

@@ -1,8 +1,9 @@
 import os
+import warnings
 import xml.etree.ElementTree as ET
 import numpy as np
-from pybdv.metadata import get_data_path, indent_xml, get_bdv_format
-from pybdv.metadata import write_affine
+
+from pybdv.metadata import get_data_path, indent_xml, get_bdv_format, get_resolution, write_affine
 
 
 def copy_xml_with_abspath(xml_in, xml_out):
@@ -121,5 +122,11 @@ def update_transformation_parameter(xml_path, parameter):
             raise ValueError("Expected all affine transformation with 12 parameters.")
     else:
         raise ValueError(f"Invalid affine transformation {parameter}")
-    write_affine(xml_path, setup_id=0, affine=parameter,
-                 overwrite=True, timepoint=0)
+    resolution = get_resolution(xml_path, setup_id=0)
+    if np.product(resolution) != 1:
+        warnings.warn(
+            f"The xml file at {xml_path} has the resolution {resolution}."
+            "The corresponding transformation will be over-written,"
+            "make sure to factor it in with the transformation you have specified."
+        )
+    write_affine(xml_path, setup_id=0, affine=parameter, overwrite=True, timepoint=0)