# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1701867835 0
# Node ID 2b3115342fefa3380809dfb6eaae2510894b7b76
# Parent  ae2f265ecf8e44aba222029414226d8815895e94
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6

diff -r ae2f265ecf8e -r 2b3115342fef common.py
--- a/common.py	Tue Nov 14 15:34:40 2023 +0000
+++ b/common.py	Wed Dec 06 13:03:55 2023 +0000
@@ -7,38 +7,145 @@
 
 
 def get_group(athena_group: AthenaGroup, key: str = None) -> Group:
+    group_keys = list(athena_group._athena_groups.keys())
     if key is None:
-        group_keys = list(athena_group._athena_groups.keys())
         key = group_keys[0]
-    return extract_athenagroup(athena_group._athena_groups[key])
+    else:
+        key = key.replace("-", "_")
+
+    try:
+        return extract_athenagroup(athena_group._athena_groups[key])
+    except KeyError as e:
+        raise KeyError(f"{key} not in {group_keys}") from e
+
+
+def read_all_groups(dat_file: str, key: str = None) -> "dict[str, Group]":
+    # Cannot rely on do_ABC as _larch is None
+    athena_group = read_athena(
+        dat_file,
+        do_preedge=False,
+        do_bkg=False,
+        do_fft=False,
+    )
+    all_groups = {}
+    for key in athena_group._athena_groups.keys():
+        group = get_group(athena_group, key)
+        pre_edge_with_defaults(group=group)
+        xftf_with_defaults(group=group)
+        all_groups[key] = group
+
+    return all_groups
+
+
+def read_group(dat_file: str, key: str = None):
+    # Cannot rely on do_ABC as _larch is None
+    athena_group = read_athena(
+        dat_file,
+        do_preedge=False,
+        do_bkg=False,
+        do_fft=False,
+    )
+    group = get_group(athena_group, key)
+    pre_edge_with_defaults(group=group)
+    xftf_with_defaults(group=group)
+    return group
 
 
-def read_group(dat_file: str, key: str = None, xftf_params: dict = None):
-    athena_group = read_athena(dat_file)
-    group = get_group(athena_group, key)
-    bkg_parameters = group.athena_params.bkg
-    print(group.athena_params.fft)
-    print(group.athena_params.fft.__dict__)
-    pre_edge(
-        group,
-        e0=bkg_parameters.e0,
-        pre1=bkg_parameters.pre1,
-        pre2=bkg_parameters.pre2,
-        norm1=bkg_parameters.nor1,
-        norm2=bkg_parameters.nor2,
-        nnorm=bkg_parameters.nnorm,
-        make_flat=bkg_parameters.flatten,
+def pre_edge_with_defaults(group: Group, settings: dict = None):
+    merged_settings = {}
+    try:
+        bkg_parameters = group.athena_params.bkg
+    except AttributeError as e:
+        print(f"Cannot load group.athena_params.bkg from group:\n{e}")
+        bkg_parameters = None
+
+    keys = (
+        ("e0", "e0", None),
+        ("pre1", "pre1", None),
+        ("pre2", "pre2", None),
+        ("norm1", "nor1", None),
+        ("norm2", "nor2", None),
+        ("nnorm", "nnorm", None),
+        ("make_flat", "flatten", None),
+        ("step", "step", None),
+        # This cannot be read from file as it is not stored by Larch (0.9.71)
+        # ("nvict", "nvict", None),
     )
-    autobk(group)
-    if xftf_params is None:
-        xftf(group)
-    else:
-        print(xftf_params)
-        xftf(group, **xftf_params)
-        xftf_details = Group()
-        setattr(xftf_details, "call_args", xftf_params)
-        group.xftf_details = xftf_details
-    return group
+    for key, parameters_key, default in keys:
+        extract_attribute(
+            merged_settings, key, bkg_parameters, parameters_key, default
+        )
+
+    if settings:
+        for k, v in settings.items():
+            if k == "nvict":
+                print(
+                    "WARNING: `nvict` can be used for pre-edge but is not "
+                    "saved to file, so value used will not be accessible in "
+                    "future operations using this Athena .prj"
+                )
+            merged_settings[k] = v
+
+    print(f"Pre-edge normalization with {merged_settings}")
+    try:
+        pre_edge(group, **merged_settings)
+    except Warning as e:
+        raise Warning(
+            "Unable to perform pre-edge fitting with:\n\n"
+            f"energy:\n{group.energy}\n\nmu:{group.mu}\n\n"
+            "Consider checking the correct columns have been extracted"
+        ) from e
+    autobk(group, pre_edge_kws=merged_settings)
+
+
+def xftf_with_defaults(group: Group, settings: dict = None):
+    merged_settings = {}
+    try:
+        fft_parameters = group.athena_params.fft
+    except AttributeError as e:
+        print(f"Cannot load group.athena_params.fft from group:\n{e}")
+        fft_parameters = None
+
+    keys = (
+        ("kmin", "kmin", 0),
+        ("kmax", "kmax", 20),
+        ("dk", "dk", 1),
+        ("kweight", "kw", 2),
+        ("kweight", "kweight", 2),
+        ("window", "kwindow", "kaiser"),
+    )
+    for key, parameters_key, default in keys:
+        extract_attribute(
+            merged_settings, key, fft_parameters, parameters_key, default
+        )
+
+    if settings:
+        for k, v in settings.items():
+            merged_settings[k] = v
+
+    print(f"XFTF with {merged_settings}")
+    xftf(group, **merged_settings)
+    xftf_details = Group()
+    setattr(xftf_details, "call_args", merged_settings)
+    group.xftf_details = xftf_details
+
+
+def extract_attribute(
+    merged_settings: dict,
+    key: str,
+    parameters_group: Group,
+    parameters_key: str,
+    default: "str|int" = None,
+):
+    if parameters_group is not None:
+        try:
+            merged_settings[key] = getattr(parameters_group, parameters_key)
+            return
+        except AttributeError:
+            pass
+
+    if default is not None:
+        merged_settings[key] = default
 
 
 def read_groups(dat_files: "list[str]", key: str = None) -> Iterable[Group]:
diff -r ae2f265ecf8e -r 2b3115342fef larch_athena.py
--- a/larch_athena.py	Tue Nov 14 15:34:40 2023 +0000
+++ b/larch_athena.py	Wed Dec 06 13:03:55 2023 +0000
@@ -4,7 +4,9 @@
 import re
 import sys
 
-from common import read_group
+from common import (
+    pre_edge_with_defaults, read_all_groups, read_group, xftf_with_defaults
+)
 
 from larch.io import (
     create_athena,
@@ -14,7 +16,7 @@
     set_array_labels,
 )
 from larch.symboltable import Group
-from larch.xafs import autobk, pre_edge, rebin_xafs, xftf
+from larch.xafs import rebin_xafs
 
 import matplotlib
 import matplotlib.pyplot as plt
@@ -27,13 +29,11 @@
         self,
         energy_column: str,
         mu_column: str,
-        xftf_params: dict,
         data_format: str,
-        extract_group: str = None,
+        extract_group: "dict[str, str]" = None,
     ):
         self.energy_column = energy_column
         self.mu_column = mu_column
-        self.xftf_params = xftf_params
         self.data_format = data_format
         self.extract_group = extract_group
 
@@ -72,13 +72,24 @@
         self,
         filepath: str,
         is_zipped: bool = False,
-    ) -> "dict[str,Group]":
+    ) -> "tuple[dict, bool]":
         if is_zipped:
             return self.load_zipped_files()
 
         print(f"Attempting to read from {filepath}")
         if self.data_format == "athena":
-            group = read_group(filepath, self.extract_group, self.xftf_params)
+            if self.extract_group["extract_group"] == "single":
+                group = read_group(filepath, self.extract_group["group_name"])
+                return {"out": group}
+            elif self.extract_group["extract_group"] == "multiple":
+                groups = {}
+                for repeat in self.extract_group["multiple"]:
+                    name = repeat["group_name"]
+                    groups[name] = read_group(filepath, name)
+                return groups
+            else:
+                return read_all_groups(filepath)
+
         else:
             # Try ascii anyway
             try:
@@ -90,7 +101,9 @@
             except (UnicodeDecodeError, TypeError):
                 # Indicates this isn't plaintext, try h5
                 group = self.load_h5(filepath)
-        return {"out": group}
+            pre_edge_with_defaults(group)
+            xftf_with_defaults(group)
+            return {"out": group}
 
     def load_ascii(self, dat_file):
         with open(dat_file) as f:
@@ -156,27 +169,27 @@
 
         if "energy" in labels:
             print("'energy' present in column headers")
-        elif self.energy_column is not None:
+        elif self.energy_column:
             if self.energy_column.lower() in labels:
                 labels[labels.index(self.energy_column.lower())] = "energy"
             else:
                 raise ValueError(f"{self.energy_column} not found in {labels}")
         else:
             for i, label in enumerate(labels):
-                if label == "col1" or label.endswith("energy"):
+                if label in ("col1", "ef") or label.endswith("energy"):
                     labels[i] = "energy"
                     break
 
         if "mu" in labels:
             print("'mu' present in column headers")
-        elif self.mu_column is not None:
+        elif self.mu_column:
             if self.mu_column.lower() in labels:
                 labels[labels.index(self.mu_column.lower())] = "mu"
             else:
                 raise ValueError(f"{self.mu_column} not found in {labels}")
         else:
             for i, label in enumerate(labels):
-                if label in ["col2", "xmu", "lni0it", "ffi0"]:
+                if label in ["col2", "xmu", "lni0it", "ffi0", "ff/i1"]:
                     labels[i] = "mu"
                     break
 
@@ -189,29 +202,24 @@
 
 def calibrate_energy(
     xafs_group: Group,
-    energy_0: float,
-    energy_min: float,
-    energy_max: float,
-    energy_format: str,
+    calibration_e0: float = None,
+    energy_min: float = None,
+    energy_max: float = None,
 ):
-    if energy_0 is not None:
-        print(f"Recalibrating energy edge from {xafs_group.e0} to {energy_0}")
-        xafs_group.energy = xafs_group.energy + energy_0 - xafs_group.e0
-        xafs_group.e0 = energy_0
+    if calibration_e0 is not None:
+        print(f"Recalibrating edge from {xafs_group.e0} to {calibration_e0}")
+        xafs_group.energy = xafs_group.energy + calibration_e0 - xafs_group.e0
+        xafs_group.e0 = calibration_e0
 
     if not (energy_min or energy_max):
         return xafs_group
 
-    if energy_min:
-        if energy_format == "relative":
-            energy_min += xafs_group.e0
+    if energy_min is not None:
         index_min = np.searchsorted(xafs_group.energy, energy_min)
     else:
         index_min = 0
 
-    if energy_max:
-        if energy_format == "relative":
-            energy_max += xafs_group.e0
+    if energy_max is not None:
         index_max = np.searchsorted(xafs_group.energy, energy_max)
     else:
         index_max = len(xafs_group.energy)
@@ -240,81 +248,57 @@
 
 def main(
     xas_data: Group,
-    input_values: dict,
+    do_calibrate: bool,
+    calibrate_settings: dict,
+    do_rebin: bool,
+    do_pre_edge: bool,
+    pre_edge_settings: dict,
+    do_xftf: bool,
+    xftf_settings: dict,
+    plot_graph: bool,
+    annotation: str,
     path_key: str = "out",
 ):
-    energy_0 = input_values["variables"]["energy_0"]
-    if energy_0 is None and hasattr(xas_data, "e0"):
-        energy_0 = xas_data.e0
-
-    energy_format = input_values["variables"]["energy_format"]
-    pre1 = input_values["variables"]["pre1"]
-    pre2 = input_values["variables"]["pre2"]
-    pre1 = validate_pre(pre1, energy_0, energy_format)
-    pre2 = validate_pre(pre2, energy_0, energy_format)
-
-    pre_edge(
-        energy=xas_data.energy,
-        mu=xas_data.mu,
-        group=xas_data,
-        e0=energy_0,
-        pre1=pre1,
-        pre2=pre2,
-    )
+    if do_calibrate:
+        print(f"Calibrating energy with {calibrate_settings}")
+        xas_data = calibrate_energy(xas_data, **calibrate_settings)
+        # After re-calibrating, will need to redo pre-edge with new range
+        do_pre_edge = True
 
-    energy_min = input_values["variables"]["energy_min"]
-    energy_max = input_values["variables"]["energy_max"]
-    xas_data = calibrate_energy(
-        xas_data,
-        energy_0,
-        energy_min,
-        energy_max,
-        energy_format=energy_format,
-    )
+    if do_rebin:
+        print("Re-binning data")
+        rebin_xafs(
+            energy=xas_data.energy,
+            mu=xas_data.mu,
+            group=xas_data,
+            **pre_edge_settings,
+        )
+        xas_data = xas_data.rebinned
+        # After re-bin, will need to redo pre-edge
+        do_pre_edge = True
 
-    if input_values["rebin"]:
-        print(xas_data.energy, xas_data.mu)
-        rebin_xafs(energy=xas_data.energy, mu=xas_data.mu, group=xas_data)
-        xas_data = xas_data.rebinned
-        pre_edge(energy=xas_data.energy, mu=xas_data.mu, group=xas_data)
+    if do_pre_edge:
+        pre_edge_with_defaults(xas_data, pre_edge_settings)
 
-    try:
-        autobk(xas_data)
-    except ValueError as e:
-        raise ValueError(
-            f"autobk failed with energy={xas_data.energy}, mu={xas_data.mu}.\n"
-            "This may occur if the edge is not included in the above ranges."
-        ) from e
-    xftf(xas_data, **xftf_params)
+    if do_xftf:
+        xftf_with_defaults(xas_data, xftf_settings)
 
-    if input_values["plot_graph"]:
+    if plot_graph:
         plot_edge_fits(f"edge/{path_key}.png", xas_data)
         plot_flattened(f"flat/{path_key}.png", xas_data)
         plot_derivative(f"derivative/{path_key}.png", xas_data)
 
     xas_project = create_athena(f"prj/{path_key}.prj")
     xas_project.add_group(xas_data)
-    if input_values["annotation"]:
+    if annotation:
         group = next(iter(xas_project.groups.values()))
-        group.args["annotation"] = input_values["annotation"]
+        group.args["annotation"] = annotation
     xas_project.save()
 
     # Ensure that we do not run out of memory when running on large zips
     gc.collect()
 
 
-def validate_pre(pre, energy_0, energy_format):
-    if pre is not None and energy_format == "absolute":
-        if energy_0 is None:
-            raise ValueError(
-                "Edge energy must be set manually or be present in the "
-                "existing Athena project if using absolute format."
-            )
-        pre -= energy_0
-
-    return pre
-
-
 def plot_derivative(plot_path: str, xafs_group: Group):
     plt.figure()
     plt.plot(xafs_group.energy, xafs_group.dmude)
@@ -363,9 +347,8 @@
         )
     else:
         is_zipped = False
-    xftf_params = input_values["variables"]["xftf"]
+
     extract_group = None
-
     if "extract_group" in input_values["merge_inputs"]["format"]:
         extract_group = input_values["merge_inputs"]["format"]["extract_group"]
 
@@ -379,7 +362,6 @@
     reader = Reader(
         energy_column=energy_column,
         mu_column=mu_column,
-        xftf_params=xftf_params,
         data_format=data_format,
         extract_group=extract_group,
     )
@@ -388,9 +370,35 @@
         merge_inputs=merge_inputs,
         is_zipped=is_zipped,
     )
+
+    calibrate_items = input_values["processing"]["calibrate"].items()
+    calibrate_settings = {k: v for k, v in calibrate_items if v is not None}
+    do_calibrate = calibrate_settings.pop("calibrate") == "true"
+
+    do_rebin = input_values["processing"].pop("rebin")
+
+    pre_edge_items = input_values["processing"]["pre_edge"].items()
+    pre_edge_settings = {k: v for k, v in pre_edge_items if v is not None}
+    do_pre_edge = pre_edge_settings.pop("pre_edge") == "true"
+
+    xftf_items = input_values["processing"]["xftf"].items()
+    xftf_settings = {k: v for k, v in xftf_items if v is not None}
+    do_xftf = xftf_settings.pop("xftf") == "true"
+
+    plot_graph = input_values["plot_graph"]
+    annotation = input_values["annotation"]
+
     for key, group in keyed_data.items():
         main(
             group,
-            input_values=input_values,
+            do_calibrate=do_calibrate,
+            calibrate_settings=calibrate_settings,
+            do_rebin=do_rebin,
+            do_pre_edge=do_pre_edge,
+            pre_edge_settings=pre_edge_settings,
+            do_xftf=do_xftf,
+            xftf_settings=xftf_settings,
+            plot_graph=plot_graph,
+            annotation=annotation,
             path_key=key,
         )
diff -r ae2f265ecf8e -r 2b3115342fef larch_athena.xml
--- a/larch_athena.xml	Tue Nov 14 15:34:40 2023 +0000
+++ b/larch_athena.xml	Wed Dec 06 13:03:55 2023 +0000
@@ -4,7 +4,7 @@
         <!-- version of underlying tool (PEP 440) -->
         <token name="@TOOL_VERSION@">0.9.71</token>
         <!-- version of this tool wrapper (integer) -->
-        <token name="@WRAPPER_VERSION@">0</token>
+        <token name="@WRAPPER_VERSION@">1</token>
         <!-- citation should be updated with every underlying tool version -->
         <!-- typical fields to update are version, month, year, and doi -->
         <token name="@TOOL_CITATION@">10.1088/1742-6596/430/1/012007</token>
@@ -15,11 +15,26 @@
             </param> 
         </xml>
         <xml name="extract_group">
-            <param name="extract_group" type="text" optional="true" label="Extract group" help="Which group to extract and process from the Athena project (will use first group in file if unset)"/>
+            <conditional name="extract_group">
+                <param name="extract_group" type="select" label="Group extraction" help="Method of handling group extraction. Extracting all or multiple named groups will result in multiple outputs, unless merging groups is also true.">
+                    <option value="single" selected="true">Extract single</option>
+                    <option value="multiple">Extract multiple</option>
+                    <option value="all">Extract all</option>
+                </param>
+                <when value="single">
+                    <param name="group_name" type="text" optional="true" label="Group label" help="Which group to extract and process from the Athena project (will use first group in file if unset)"/>
+                </when>
+                <when value="multiple">
+                    <repeat name="multiple" min="1" default="1" title="Groups">
+                        <param name="group_name" type="text" label="Group label" help="Which group to extract and process from the Athena project (will use first group in file if unset)"/>
+                    </repeat>
+                </when>
+                <when value="all"/>
+            </conditional>
         </xml>
         <xml name="columns">
-            <param name="energy_column" type="text" optional="true" label="Energy column" help="If set, this column we be used as 'energy'. Otherwise, will identify columns ending with 'energy' or labelled 'col1'."/>
-            <param name="mu_column" type="text" optional="true" label="μ column" help="If set, this column we be used as 'mu'. Otherwise, will identify the first column labelled as either 'col2', 'xmu', 'lni0it' or 'FFI0'."/>
+            <param name="energy_column" type="text" optional="true" label="Energy column" help="If set, this column we be used as 'energy'. Otherwise, will identify the first column ending with 'energy' or labelled 'col1' 'Ef'."/>
+            <param name="mu_column" type="text" optional="true" label="μ column" help="If set, this column we be used as 'mu'. Otherwise, will identify the first column labelled as either 'col2', 'xmu', 'lni0it', 'FFI0' or 'FF/I1'."/>
         </xml>
         <xml name="is_zipped">
             <param name="is_zipped" type="select" display="radio" label="Inputs Zipped" help="Whether plaintext input files are zipped together into one directory, or not.">
@@ -40,6 +55,7 @@
     </requirements>
     <required_files>
         <include type="literal" path="larch_athena.py"/>
+        <include type="literal" path="common.py"/>
     </required_files>
     <command detect_errors="exit_code"><![CDATA[
         mkdir prj edge flat derivative
@@ -111,16 +127,55 @@
             </when>
         </conditional>
         <param name="annotation" type="text" label="Annotation" optional="true" help="If set, will annotate the output project(s) with this string. This will be used to generate legends when plotting data."/>
-        <section name="variables" title="Processing Options">
-            <param name="energy_0" type="float" label="Edge energy (eV)" optional="true" help="If set, data will be calibrated so that the edge occurs at this energy (after merging, if relevant)."/>
-            <expand macro="energy_limits"/>
-            <param name="pre1" type="float" label="Pre-edge fit lower energy (eV)" optional="true" help="The lower edge of the region used for the pre-edge fitting, if unset will either use existing value or a default based on the data."/>
-            <param name="pre2" type="float" label="Pre-edge fit upper energy (eV)" optional="true" help="The upper edge of the region used for the pre-edge fitting, if unset will either use existing value or a default based on the data."/>
-            <section name="xftf" title="XFTF">
-                <expand macro="xftf_params"/>
-            </section>
+        <section name="processing" expanded="true" title="Processing Options" help="By default, the following processing steps will be performed either with default values, or those contained in the input Athena project (if used). If specified here, these values will be used instead for process in sequence.">
+            <conditional name="calibrate">
+                <param name="calibrate" type="select" label="Calibrate energy" help="If set, will shift the spectrum so that its (automatically determined) edge occurs at the specified value, and any values outside the range will be discarded.">
+                    <option value="" selected="true">False</option>
+                    <option value="true">True</option>
+                </param>
+                <when value=""/>
+                <when value="true">
+                    <param name="calibration_e0" type="float" label="Calibration energy (eV)" optional="true" help="If set, data will be calibrated so that the edge occurs at this energy (after merging, if relevant). Note that this is different from specifying E0 in the pre-edge normalization, as this will the x-axis of the data (so that the Nth x point will no longer align with the Nth y point)."/>
+                    <param name="energy_min" type="float" label="Minimum energy (eV)" optional="true" help="If set, data will be cropped below this value in electron volts (after re-calibrating)."/>
+                    <param name="energy_max" type="float" label="Maximum energy (eV)" optional="true" help="If set, data will be cropped above this value in electron volts (after re-calibrating)."/>
+                </when>
+            </conditional>
+            <param name="rebin" type="boolean" label="Re-bin data" help="Whether to re-bin along the energy axis to automatically ensure appropriate levels of precision in the pre-edge, near-edge and extended region of the spectrum."/>
+            <conditional name="pre_edge">
+                <param name="pre_edge" type="select" label="Pre-edge normalization" help="If set, will (re)perform forward pre-edge normalization using provided values.">
+                    <option value="" selected="true">False</option>
+                    <option value="true">True</option>
+                </param>
+                <when value=""/>
+                <when value="true">
+                    <param argument="e0" type="float" label="Edge energy (eV)" optional="true" help="If set, normalization will use this as the location of the edge rather than automatically determining it."/>
+                    <param argument="pre1" type="float" max="0" label="Pre-edge fit lower energy (eV)" optional="true" help="The lower end of the region used for the pre-edge fitting, relative to the edge energy (and therefore negative)."/>
+                    <param argument="pre2" type="float" max="0" label="Pre-edge fit upper energy (eV)" optional="true" help="The upper end of the region used for the pre-edge fitting, relative to the edge energy (and therefore negative)."/>
+                    <param argument="nvict" type="integer" label="Energy exponent" optional="true" help="Edge fitting will be performed against μ*E**n where n is defined here. This is 0 by default."/>
+                </when>
+            </conditional>
+            <conditional name="xftf">
+                <param name="xftf" type="select" label="XFTF" help="If set, will (re)perform forward Fourier Transform using provided values.">
+                    <option value="" selected="true">False</option>
+                    <option value="true">True</option>
+                </param>
+                <when value=""/>
+                <when value="true">
+                    <param argument="kmin" type="float" optional="true" min="0.0" help="Minimum k value."/>
+                    <param argument="kmax" type="float" optional="true" min="0.0" help="Maximum k value."/>
+                    <param argument="kweight" type="float" optional="true" help="Exponent for weighting spectra by raising k to this power."/>
+                    <param argument="dk" type="float" optional="true" help="Tapering parameter for Fourier Transform window."/>
+                    <param argument="window" type="select" optional="true" help="Fourier Transform window type.">
+                        <option value="hanning">Hanning (cosine-squared taper)</option>
+                        <option value="parzen">Parzen (linear taper)</option>
+                        <option value="welch">Welch (quadratic taper)</option>
+                        <option value="gaussian">Gaussian function window</option>
+                        <option value="sine">Sine function window</option>
+                        <option value="kaiser">Kaiser-Bessel function-derived window</option>
+                    </param>
+                </when>
+            </conditional>
         </section>
-        <param name="rebin" type="boolean" label="Re-bin data" help="Whether to re-bin along the energy axis to ensure appropriate levels of precision in the pre-edge, near-edge and extended region of the spectrum."/>
         <param name="plot_graph" type="boolean" label="Plot graph" help="Whether to plot the pre/post edge fitting and the normalised xμ data."/>
         <param name="zip_outputs" type="boolean" label="Zip outputs" help="Whether to zip all outputs into one dataset."/>
     </inputs>
@@ -129,53 +184,53 @@
         <data name="out_zip" format="zip" from_work_dir="out_zip.zip" label="Zipped Athena project(s) ${annotation} ${on_string}">
             <filter>zip_outputs</filter>
         </data>
-        <!-- Single outputs of differnt types if merging, or not using a zip -->
+        <!-- Single outputs of different types if merging, or not using a zip -->
         <data name="athena_project_file" format="prj" from_work_dir="prj/out.prj" label="Athena project ${annotation} ${on_string}">
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] or (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"] == "")</filter>
+            <filter>not (merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
         </data>
         <data name="edge_plot" format="png" from_work_dir="edge/out.png" label="Edge fitting ${annotation} ${on_string}">
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] or (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"] == "")</filter>
+            <filter>not (merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
         </data>
         <data name="flat_plot" format="png" from_work_dir="flat/out.png" label="Flattened plot ${annotation} ${on_string}">
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] or (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"] == "")</filter>
+            <filter>not (merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
         </data>
         <data name="derivative_plot" format="png" from_work_dir="derivative/out.png" label="Derivative plot ${annotation} ${on_string}">
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] or merge_inputs["format"]["dat_file"].extension != "zip"</filter>
-            <filter>merge_inputs["merge_inputs"] or (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"] == "")</filter>
+            <filter>not (merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single"))</filter>
         </data>
-        <!-- Directories of outputs if using single, non-merged zip as input -->
+        <!-- Directories of outputs if using single, non-merged zip as input or extracting multiple/all Athena groups -->
         <collection name="athena_project_file_collection" format="prj" type="list" label="Athena projects ${annotation} ${on_string}">
             <discover_datasets pattern="__name_and_ext__" directory="prj"/>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] == "" and merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]</filter>
+            <filter>merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")</filter>
         </collection>
         <collection name="edge_plot_collection" format="png" type="list" label="Edge fittings ${annotation} ${on_string}">
             <discover_datasets pattern="__name_and_ext__" directory="edge"/>
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] == "" and merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]</filter>
+            <filter>merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")</filter>
         </collection>
         <collection name="flat_plot_collection" format="png" type="list" label="Flattened plots ${annotation} ${on_string}">
             <discover_datasets pattern="__name_and_ext__" directory="flat"/>
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] == "" and merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]</filter>
+            <filter>merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")</filter>
         </collection>
         <collection name="derivative_plot_collection" format="png" type="list" label="Derivative plots ${annotation} ${on_string}">
             <discover_datasets pattern="__name_and_ext__" directory="derivative"/>
             <filter>plot_graph</filter>
             <filter>not zip_outputs</filter>
-            <filter>merge_inputs["merge_inputs"] == "" and merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]</filter>
+            <filter>merge_inputs["merge_inputs"] == "" and (merge_inputs["format"]["format"] == "plaintext" and merge_inputs["format"]["is_zipped"]["is_zipped"]) or (merge_inputs["format"]["format"] == "athena" and merge_inputs["format"]["extract_group"]["extract_group"] != "single")</filter>
         </collection>
     </outputs>
     <tests>
+        <!-- 1 -->
         <test expect_num_outputs="1">
             <param name="dat_file" value="test.xmu"/>
             <output name="athena_project_file">
@@ -184,6 +239,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 2 -->
         <test expect_num_outputs="1">
             <param name="dat_file" value="ffi0.tabular"/>
             <output name="athena_project_file">
@@ -192,12 +248,22 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 3 -->
+        <test expect_num_outputs="1">
+            <param name="dat_file" value="ffi1.tabular"/>
+            <output name="athena_project_file">
+                <assert_contents>
+                    <has_size value="4400" delta="100"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- 4 -->
         <test expect_num_outputs="4">
             <param name="dat_file" value="test.xmu"/>
             <param name="plot_graph" value="true"/>
             <output name="athena_project_file">
                 <assert_contents>
-                    <has_size value="5405" delta="10"/>
+                    <has_size value="5400" delta="100"/>
                 </assert_contents>
             </output>
             <output name="edge_plot">
@@ -216,6 +282,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 5 -->
         <test expect_num_outputs="4">
             <param name="is_zipped" value="true"/>
             <param name="dat_file" value="test.zip"/>
@@ -225,6 +292,7 @@
             <output_collection name="flat_plot_collection" type="list" count="2"/>
             <output_collection name="derivative_plot_collection" type="list" count="2"/>
         </test>
+        <!-- 6 -->
         <test expect_num_outputs="1">
             <param name="is_zipped" value="true"/>
             <param name="dat_file" value="h5.zip"/>
@@ -236,9 +304,10 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 7 -->
         <test expect_num_outputs="1">
             <param name="dat_file" value="test.xmu"/>
-            <param name="energy_format" value="absolute"/>
+            <param name="calibrate" value="true"/>
             <param name="energy_min" value="7000"/>
             <output name="athena_project_file">
                 <assert_contents>
@@ -246,9 +315,10 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 8 -->
         <test expect_num_outputs="4">
             <param name="dat_file" value="test.xmu"/>
-            <param name="energy_format" value="absolute"/>
+            <param name="calibrate" value="true"/>
             <param name="energy_min" value="7000"/>
             <param name="energy_max" value="7200"/>
             <param name="plot_graph" value="true"/>
@@ -259,32 +329,34 @@
             </output>
             <output name="edge_plot">
                 <assert_contents>
-                    <has_size value="44430" delta="10"/>
+                    <has_size value="44900" delta="100"/>
                 </assert_contents>
             </output>
             <output name="flat_plot">
                 <assert_contents>
-                    <has_size value="37310" delta="10"/>
+                    <has_size value="39400" delta="100"/>
                 </assert_contents>
             </output>
             <output name="derivative_plot">
                 <assert_contents>
-                    <has_size value="46390" delta="10"/>
+                    <has_size value="45900" delta="100"/>
                 </assert_contents>
             </output>
         </test>
+        <!-- 9 -->
         <test expect_num_outputs="1">
             <param name="dat_file" value="test.xmu"/>
-            <param name="energy_format" value="absolute"/>
-            <param name="energy_0" value="7050"/>
+            <param name="calibrate" value="true"/>
+            <param name="calibration_e0" value="7050"/>
             <param name="energy_min" value="7000"/>
             <param name="energy_max" value="7200"/>
             <output name="athena_project_file">
                 <assert_contents>
-                    <has_size value="3300" delta="50"/>
+                    <has_size value="3600" delta="100"/>
                 </assert_contents>
             </output>
         </test>
+        <!-- 10 -->
         <test expect_num_outputs="1">
             <param name="dat_file" value="test.xmu"/>
             <param name="rebin" value="true"/>
@@ -294,6 +366,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 11 -->
         <test expect_num_outputs="1">
             <param name="merge_inputs" value="true"/>
             <param name="dat_file" value="262875_PtSn_OCO_Abu_1.nxs,262876_PtSn_OCO_Abu_2.nxs"/>
@@ -303,6 +376,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 12 -->
         <test expect_num_outputs="1">
             <param name="merge_inputs" value="true"/>
             <param name="is_zipped" value="true"/>
@@ -313,6 +387,7 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 13 -->
         <test expect_num_outputs="1">
             <param name="format" value="athena"/>
             <param name="dat_file" value="test.prj"/>
@@ -322,6 +397,22 @@
                 </assert_contents>
             </output>
         </test>
+        <!-- 14: Extract multiple groups from Athena .prj -->
+        <test expect_num_outputs="1">
+            <param name="format" value="athena"/>
+            <param name="extract_group" value="multiple"/>
+            <param name="group_name" value="merge"/>
+            <param name="group_name" value="d__Ref_PtSn_OC_MERGE_CALIBRATE"/>
+            <param name="dat_file" value="multiple.prj"/>
+            <output_collection name="athena_project_file_collection" type="list" count="2"/>
+        </test>
+        <!-- 15: Extract all groups from Athena .prj -->
+        <test expect_num_outputs="1">
+            <param name="format" value="athena"/>
+            <param name="extract_group" value="all"/>
+            <param name="dat_file" value="multiple.prj"/>
+            <output_collection name="athena_project_file_collection" type="list" count="9"/>
+        </test>
     </tests>
     <help><![CDATA[
         Using Larch, create an Athena project file from the input X-ray Absorption Fine Structure (XAFS) data file.
diff -r ae2f265ecf8e -r 2b3115342fef macros.xml
--- a/macros.xml	Tue Nov 14 15:34:40 2023 +0000
+++ b/macros.xml	Wed Dec 06 13:03:55 2023 +0000
@@ -1,26 +1,6 @@
 <macros>
-    <xml name="energy_limits">
-        <param name="energy_format" type="select" display="radio" label="Energy limits" help="Whether to limit the energy relative to the absorption edge or with absolute values.">
-            <option value="relative" selected="true">Relative</option>
-            <option value="absolute">Absolute</option>
-        </param>
-        <param name="energy_min" type="float" label="Minimum energy (eV)" optional="true" help="If set, data will be cropped below this value in electron volts."/>
-        <param name="energy_max" type="float" label="Maximum energy (eV)" optional="true" help="If set, data will be cropped above this value in electron volts."/>
-    </xml>
-    <xml name="xftf_params">
-        <param argument="kmin" type="float" value="0" min="0.0" help="Minimum k value."/>
-        <param argument="kmax" type="float" value="20" min="0.0" help="Maximum k value."/>
-        <param argument="kweight" type="float" value="2" help="Exponent for weighting spectra by raising k to this power."/>
-        <param argument="dk" type="float" value="4" help="Tapering parameter for Fourier Transform window."/>
-        <param argument="window" type="select" help="Fourier Transform window type.">
-            <option value="hanning">Hanning (cosine-squared taper)</option>
-            <option value="parzen">Parzen (linear taper)</option>
-            <option value="welch">Welch (quadratic taper)</option>
-            <option value="gaussian">Gaussian function window</option>
-            <option value="sine">Sine function window</option>
-            <option value="kaiser" selected="true">Kaiser-Bessel function-derived window</option>
-        </param>
-        <param argument="rmin" type="float" value="0.0" min="0.0" help="Minimum radial distance."/>
-        <param argument="rmax" type="float" value="10.0" min="0.0" help="Maximum radial distance."/>
+    <xml name="plot_limits_energy">
+        <param name="x_limit_min" type="float" label="Minimum plot energy (eV)" optional="true" help="If set, plot will be limited to this value on the x axis."/>
+        <param name="x_limit_max" type="float" label="Maximum plot energy (eV)" optional="true" help="If set, plot will be limited to this value on the x axis."/>
     </xml>
 </macros>
\ No newline at end of file
diff -r ae2f265ecf8e -r 2b3115342fef test-data/ffi1.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ffi1.tabular	Wed Dec 06 13:03:55 2023 +0000
@@ -0,0 +1,355 @@
+# Energy        	FF/I1       	Time
+  6911.8277       0.80926541        272002.00
+  6916.9236       0.80418730        270032.00
+  6921.7638       0.79959074        268827.00
+  6926.8750       0.79459529        267514.00
+  6931.7907       0.79004613        255214.00
+
+  6962.0000       0.78791063        305150.00
+  6972.0000       0.77475191        306445.00
+  6982.0000       0.76169076        306446.00
+  6992.0000       0.74992551        306744.00
+  7002.0000       0.73660315        306246.00
+  7012.0000       0.72423404        306358.00
+  7022.0000       0.71196509        306309.00
+  7032.0000       0.70002723        306019.00
+  7042.0000       0.68735767        306529.00
+  7052.0000       0.67439453        306124.00
+  7062.0000       0.66235517        306188.00
+  7072.0000       0.65022361        306119.00
+  7082.0000       0.63942705        306143.00
+  7092.0000       0.62824650        306098.00
+  7092.5000       0.62753795        305825.00
+  7093.0000       0.62748380        305756.00
+  7093.5000       0.62785219        305745.00
+  7094.0000       0.62636441        305717.00
+  7094.5000       0.62575793        305670.00
+  7095.0000       0.62551244        305666.00
+  7095.5000       0.62515947        305631.00
+  7096.0000       0.62492947        305585.00
+  7096.5000       0.62367544        305536.00
+  7097.0000       0.62332504        305539.00
+  7097.5000       0.62259547        305510.00
+  7098.0000       0.62252464        305466.00
+  7098.5000       0.62240279        305494.00
+  7099.0000       0.62172416        305432.00
+  7099.5000       0.62098768        305503.00
+  7100.0000       0.62118707        305402.00
+  7100.5000       0.62045272        305414.00
+  7101.0000       0.62040785        305391.00
+  7101.5000       0.62002332        305400.00
+  7102.0000       0.61932445        305952.00
+  7102.5000       0.61954721        305420.00
+  7103.0000       0.61934375        304860.00
+  7103.5000       0.61907141        305180.00
+  7104.0000       0.61843263        305180.00
+  7104.5000       0.61879967        305435.00
+  7105.0000       0.61854579        305144.00
+  7105.5000       0.61837948        305045.00
+  7106.0000       0.61887282        304943.00
+  7106.5000       0.61837848        305015.00
+  7107.0000       0.61844121        305023.00
+  7107.5000       0.61908174        304990.00
+  7108.0000       0.62025344        305117.00
+  7108.5000       0.62083284        305305.00
+  7109.0000       0.62279082        304852.00
+  7109.5000       0.62484776        304938.00
+  7110.0000       0.63029578        305214.00
+  7110.5000       0.63827614        304831.00
+  7111.0000       0.65354125        304668.00
+  7111.5000       0.67171017        304489.00
+  7112.0000       0.68465719        304804.00
+  7112.5000       0.68977450        304821.00
+  7113.0000       0.68982223        304700.00
+  7113.5000       0.68880150        304652.00
+  7114.0000       0.68631667        304907.00
+  7114.5000       0.68636382        304536.00
+  7115.0000       0.69345881        305540.00
+  7115.5000       0.71368054        306249.00
+  7116.0000       0.75470012        306100.00
+  7116.5000       0.82334644        305917.00
+  7117.0000       0.91897755        306536.00
+  7117.5000        1.0048919        306925.00
+  7118.0000        1.0613446        306741.00
+  7118.5000        1.1171460        306475.00
+  7119.0000        1.1598287        306428.00
+  7119.5000        1.1845153        306460.00
+  7120.0000        1.1839175        306450.00
+  7120.5000        1.1705836        306582.00
+  7121.0000        1.1532435        306359.00
+  7121.5000        1.1455536        306364.00
+  7122.0000        1.1474359        306349.00
+  7122.5000        1.1522733        306255.00
+  7123.0000        1.1570854        306266.00
+  7123.5000        1.1609012        306230.00
+  7124.0000        1.1633654        306227.00
+  7124.5000        1.1626865        306371.00
+  7125.0000        1.1609214        306051.00
+  7125.5000        1.1630846        306141.00
+  7126.0000        1.1694208        306113.00
+  7126.5000        1.1791744        306099.00
+  7127.0000        1.1920499        306090.00
+  7127.5000        1.2050365        306010.00
+  7128.0000        1.2176110        306003.00
+  7128.5000        1.2307236        305954.00
+  7129.0000        1.2447142        305942.00
+  7129.5000        1.2590796        306047.00
+  7130.0000        1.2750382        305942.00
+  7130.5000        1.2916155        305940.00
+  7131.0000        1.3069910        305777.00
+  7131.5000        1.3214558        305771.00
+  7132.0000        1.3316754        305988.00
+  7132.8830        1.3507457        305946.00
+  7133.7850        1.3673679        305893.00
+  7134.7070        1.3796873        305719.00
+  7135.6470        1.3878931        305734.00
+  7136.6060        1.3912805        305686.00
+  7137.5840        1.3911931        305808.00
+  7138.5820        1.3880279        305655.00
+  7139.5990        1.3853474        305680.00
+  7140.6340        1.3831500        305655.00
+  7141.6890        1.3775299        305647.00
+  7142.7630        1.3673370        305546.00
+  7143.8560        1.3502223        305620.00
+  7144.9680        1.3336271        305565.00
+  7146.0990        1.3195536        305942.00
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\ No newline at end of file
diff -r ae2f265ecf8e -r 2b3115342fef test-data/multiple.prj
Binary file test-data/multiple.prj has changed