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removing x-ray utils in from xrd reader.
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@RubelMozumder
RubelMozumder committed Nov 28, 2023
1 parent 423082c commit c593c92
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Showing 5 changed files with 138 additions and 42 deletions.
12 changes: 3 additions & 9 deletions dev-requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#
# This file is autogenerated by pip-compile with Python 3.10
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
# pip-compile --extra=dev --output-file=dev-requirements.txt pyproject.toml
Expand Down Expand Up @@ -104,7 +104,6 @@ h5py==3.7.0
# pyfai
# pynxtools (pyproject.toml)
# silx
# xrayutilities
hyperspy==1.7.4
# via
# kikuchipy
Expand Down Expand Up @@ -167,9 +166,7 @@ lazy-object-proxy==1.9.0
llvmlite==0.39.1
# via numba
lmfit==1.2.0
# via
# pyxem
# xrayutilities
# via pyxem
locket==1.0.0
# via partd
markupsafe==2.1.1
Expand Down Expand Up @@ -279,7 +276,6 @@ numpy==1.21.6
# sparse
# tifffile
# xarray
# xrayutilities
# zarr
numpy-quaternion==2022.4.3
# via orix
Expand Down Expand Up @@ -436,7 +432,6 @@ scipy==1.7.3
# scikit-image
# scikit-learn
# sparse
# xrayutilities
silx==1.1.2
# via pyfai
six==1.16.0
Expand Down Expand Up @@ -515,6 +510,7 @@ typing-extensions==4.3.0
# astroid
# mypy
# numcodecs
# pylint
tzdata==2023.3
# via pytz-deprecation-shim
tzlocal==4.3
Expand All @@ -541,8 +537,6 @@ wrapt==1.14.1
# via astroid
xarray==0.20.2
# via pynxtools (pyproject.toml)
xrayutilities==1.7.6
# via pynxtools (pyproject.toml)
zarr==2.12.0
# via hyperspy
zipfile37==0.1.3
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36 changes: 27 additions & 9 deletions pynxtools/dataconverter/readers/xrd/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,27 +6,45 @@
"@units": "",
"@chi_indices": 0},
},
"/ENTRY[entry]/2theta_plot/intensity": {"xrdml_1.5": {"value": "/detector",
"@units": ""}
"/ENTRY[entry]/2theta_plot/intensity": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/intensities",
"@units": "counts/s"}
},
"/ENTRY[entry]/2theta_plot/omega": {"xrdml_1.5": {"value": "/Omega",
"/ENTRY[entry]/2theta_plot/omega": {"xrdml_1.5": {"value": "",
"@units": "",
"@omega_indices": 1},
},
"/ENTRY[entry]/2theta_plot/title": "Intensity Vs. Two Theta (deg.)",
"/ENTRY[entry]/2theta_plot/phi": {"xrdml_1.5": {"value": "/Omega",
"/ENTRY[entry]/2theta_plot/phi": {"xrdml_1.5": {"value": "",
"@units": "",
"@phi_indices": 0},
},
"/ENTRY[entry]/2theta_plot/two_theta": {"xrdml_1.5": {"value": "/2Theta",
"/ENTRY[entry]/2theta_plot/two_theta": {"xrdml_1.5": {"value": "",
"@units": "deg",
"@two_theta_indices": 0},
},
"/ENTRY[entry]/COLLECTION[collection]/beam_attenuation_factors": {"xrdml_1.5": {"value": "/beamAttenuationFactors",
"@units": ""},
},
"/ENTRY[entry]/COLLECTION[collection]/count_time": {"xrdml_1.5": {"value": "/countTime",
"@units": ""},
"/ENTRY[entry]/COLLECTION[collection]/omega/start": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_2/startPosition",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_2/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/omega/end": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_2/endPosition",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_2/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/omega/step": {"xrdml_1.5": {"value": "/xrdMeasurements/comment/entry_2/MinimumstepsizeOmega",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_2/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/2theta/start": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_1/startPosition",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_1/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/2theta/end": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_1/endPosition",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_1/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/2theta/step": {"xrdml_1.5": {"value": "/xrdMeasurements/comment/entry_2/Minimumstepsize2Theta",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/positions_1/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/count_time": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/commonCountingTime",
"@units": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/commonCountingTime/unit"},
},
"/ENTRY[entry]/COLLECTION[collection]/data_file": {"xrdml_1.5": {"value": ""}
},
Expand Down Expand Up @@ -88,8 +106,8 @@
},
"/ENTRY[entry]/definition": "NXxrd_pan",
"/ENTRY[entry]/method": "X-Ray Diffraction (XRD)",
"/ENTRY[entry]/q_plot/intensity": {"xrdml_1.5": {"value": "/detector",
"@units": ""},
"/ENTRY[entry]/q_plot/intensity": {"xrdml_1.5": {"value": "/xrdMeasurements/xrdMeasurement/scan/dataPoints/intensities",
"@units": "counts/s"},
},
"/ENTRY[entry]/q_plot/q": {"xrdml_1.5": {"value": "",
"@units": ""},
Expand Down
33 changes: 29 additions & 4 deletions pynxtools/dataconverter/readers/xrd/xrd_helper.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,9 +101,33 @@ def fill_template_from_config_data(config_dict: dict, template: Template,
template[nx_key] = val

def two_theta_plot():
two_theta_gr = "/ENTRY[entry]/2theta_plot"

intesity = transform_to_intended_dt(template.get("/ENTRY[entry]/2theta_plot/intensity",
None))
if intesity is not None:
intsity_len = np.shape(intesity)[0]
else:
raise ValueError("No intensity is found")

two_theta_gr = "/ENTRY[entry]/2theta_plot/"
if template.get(f"{two_theta_gr}omega", None) is None:
omega_start = template.get("/ENTRY[entry]/COLLECTION[collection]/omega/start", None)
omega_end = template.get("/ENTRY[entry]/COLLECTION[collection]/omega/end", None)

template["/ENTRY[entry]/2theta_plot/omega"] = np.linspace(float(omega_start),
float(omega_end),
intsity_len)

if template.get(f"{two_theta_gr}two_theta", None) is None:
tw_theta_start = template.get("/ENTRY[entry]/COLLECTION[collection]/2theta/start",
None)
tw_theta_end = template.get("/ENTRY[entry]/COLLECTION[collection]/2theta/end", None)
template[f"{two_theta_gr}two_theta"] = np.linspace(float(tw_theta_start),
float(tw_theta_end),
intsity_len)
template[two_theta_gr + "/" + "@axes"] = ["two_theta"]
template[two_theta_gr + "/" + "@signal"] = "intensity"
template[two_theta_gr + "/" + "@auxiliary_signals"] = "omega"

def q_plot():
q_plot_gr = "/ENTRY[entry]/q_plot"
Expand All @@ -112,13 +136,14 @@ def q_plot():
alpha_1 = template.get("/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/k_alpha_one",
None)
two_theta: np.ndarray = template.get("/ENTRY[entry]/2theta_plot/two_theta", None)
if two_theta is None:
raise ValueError("Two-theta data is not found")
if isinstance(two_theta, np.ndarray):
theta: np.ndarray = two_theta / 2
# pylint: disable=line-too-long
ratio_key = "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone"
ratio_k = "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source]/ratio_k_alphatwo_k_alphaone"
if alpha_1 and alpha_2:
ratio = alpha_2 / alpha_1
template[ratio_key] = ratio
template[ratio_k] = ratio
lamda = ratio * alpha_1 + (1 - ratio) * alpha_2
q_vec = (4 * np.pi / lamda) * np.sin(np.deg2rad(theta))
template[q_plot_gr + "/" + "q_vec"] = q_vec
Expand Down
98 changes: 79 additions & 19 deletions pynxtools/dataconverter/readers/xrd/xrd_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,8 @@
# See the License for the specific language governing permissions and
# limitations under the License.

from typing import Any, Dict, Tuple, Optional, List

from pathlib import Path
import warnings
import xml.etree.ElementTree as ET # for XML parsing
Expand Down Expand Up @@ -107,11 +109,11 @@ def handle_with_panalytical_module(self):
comes with xml file.
"""
self.parse_each_elm(parent_path='/', xml_node=self.xml_root)

nested_data_dict: Dict[str, any] = {}
# Extract other numerical data e.g. 'hkl', 'Omega', '2Theta', CountTime etc
# using panalytical_xml module
parsed_data = XRDMLFile(self.__file_path)
nested_data_dict = parsed_data.scan.ddict
# parsed_data = XRDMLFile(self.__file_path)
# nested_data_dict = parsed_data.scan.ddict
fill_slash_sep_dict_from_nested_dict('/', nested_data_dict, self.__xrd_dict)

def process_node_text(self, parent_path, node_txt) -> None:
Expand Down Expand Up @@ -152,7 +154,9 @@ def process_node_text(self, parent_path, node_txt) -> None:
warnings.warn(f'Element text {node_txt} is ignored from parseing!',
IgnoreNodeTextWarning)

def parse_each_elm(self, parent_path, xml_node):
def parse_each_elm(self, parent_path, xml_node,
multi_childs_tag: str = '',
tag_extensions: Optional[List[int]] = None):
"""Check each xml element and send the element to intended function.
Parameters
Expand All @@ -161,40 +165,86 @@ def parse_each_elm(self, parent_path, xml_node):
Path to be in the starting of the key composing from element e.g. '/'.
xml_node : XML.Element
Any element except process instruction nodes.
multi_childs_tag : str
Tag that is available on several child nodes.
tag_extension : List[int]
List of extension of the child tag if there are several childs having the same
tag.
Returns
------
None
"""

tag = remove_namespace_from_tag(xml_node.tag)
# Take care of special node of 'entry' tag
if tag == 'entry':
parent_path = self.parse_entry_elm(parent_path, xml_node)
parent_path = self.parse_entry_elm(parent_path, xml_node,
multi_childs_tag, tag_extensions)
else:
parent_path = self.parse_general_elm(parent_path, xml_node)
parent_path = self.parse_general_elm(parent_path, xml_node,
multi_childs_tag, tag_extensions)

_, multi_childs_tag = self.has_multi_childs_with_same_tag(xml_node)
# List of tag extensions for child nodes which have the same tag.
tag_extensions: List[int] = [0]
for child in iter(xml_node):
if child is not None:
self.parse_each_elm(parent_path, child)
self.parse_each_elm(parent_path, child,
multi_childs_tag, tag_extensions)

def parse_general_elm(self, parent_path, xml_node):
"""Handle general element except entry element.
def has_multi_childs_with_same_tag(self, parent_node: ET.Element) -> Tuple[str, bool]:
"""Check for multiple childs that have the same tag.
Parameter:
----------
parent_node : ET.Element
Parent node that might has multiple childs with the same tag.
Returns:
--------
Tuple[bool, str]
(true if multiple childs with the same tag, tag).
"""
tag: str = None
for child in iter(parent_node):
temp_tag = remove_namespace_from_tag(child.tag)
if tag is None:
tag = temp_tag
else:
if tag == temp_tag:
return (True, tag)

return (False, '')

def parse_general_elm(self, parent_path, xml_node,
multi_childs_tag, tag_extensions: List[int]):
"""Handle general element except entry element.
Parameters
----------
parent_path : str
Path to be in the starting of the key composing from element e.g. '/'.
xml_node : XML.Element
Any element except process instruction and entry nodes.
multi_childs_tag : str
Tag that is available on several siblings.
tag_extension : List[int]
List of extension of the shiblings tag if there are several shiblings having
the same tag.
Returns
-------
None
"""

tag = remove_namespace_from_tag(xml_node.tag)
if tag == multi_childs_tag:
new_ext = tag_extensions[-1] + 1
tag = tag + '_' + str(new_ext)
tag_extensions.append(new_ext)

if parent_path == '/':
parent_path = '/' + tag
parent_path = parent_path + tag
else:
# New parent path ends with element tag
parent_path = '/'.join([parent_path, tag])
Expand All @@ -214,7 +264,8 @@ def parse_general_elm(self, parent_path, xml_node):

return parent_path

def parse_entry_elm(self, parent_path, xml_node):
def parse_entry_elm(self, parent_path: str, xml_node: ET.Element,
multi_childs_tag: str, tag_extensions: List[int]):
"""Handle entry element.
Parameters
Expand All @@ -223,14 +274,25 @@ def parse_entry_elm(self, parent_path, xml_node):
Path to be in the starting of the key composing from element e.g. '/'.
xml_node : XML.Element
Any entry node.
multi_childs_tag : str
Tag that is available on several siblings.
tag_extension : List[int]
List of extension of the shiblings tag if there are several shiblings having
the same tag.
Returns
-------
str:
Parent path.
"""

tag = remove_namespace_from_tag(xml_node.tag)

if tag == multi_childs_tag:
new_ext = tag_extensions[-1] + 1
tag_extensions.append(new_ext)
tag = tag + '_' + str(new_ext)

if parent_path == '/':
parent_path = '/' + tag
else:
Expand Down Expand Up @@ -335,14 +397,12 @@ def parse_and_populate_template(self, template, config_dict, eln_dict):
None
"""

file_format = self.get_file_format()
if file_format == ".xrdml":
xrd_dict = self.parse()
if len(config_dict) == 0 and self.file_parser.xrdml_version == '1.5':
from pynxtools.dataconverter.readers.xrd.config import xrdml
config_dict = xrdml
feed_xrdml_to_template(template, xrd_dict, eln_dict,
file_term=self.file_term, config_dict=config_dict)
xrd_dict = self.parse()
if len(config_dict) == 0 and self.file_parser.xrdml_version == '1.5':
from pynxtools.dataconverter.readers.xrd.config import xrdml
config_dict = xrdml
feed_xrdml_to_template(template, xrd_dict, eln_dict,
file_term=self.file_term, config_dict=config_dict)

def parse(self):
'''Parses the file based on its format.
Expand Down
1 change: 0 additions & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,6 @@ dependencies = [
"tzlocal<=4.3",
"scipy>=1.7.1",
"lark>=1.1.5",
"xrayutilities>=1.7.4",
"requests",
"requests_cache",
"nanonispy@git+https://github.com/ramav87/nanonispy.git@a0da87c58482d29624a2bf5deecb763dd1274212",
Expand Down

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