Export hdf5 to zip

src/freesas/app/extract_ascii.py

@@ -26,8 +26,8 @@
 
 __author__ = "Jérôme Kieffer"
 __license__ = "MIT"
-__copyright__ = "2020, ESRF"
-__date__ = "15/01/2021"
+__copyright__ = "2020-2024, ESRF"
+__date__ = "16/04/2025"
 
 import io
 import os
@@ -38,6 +38,7 @@
 import posixpath
 from collections import namedtuple, OrderedDict
 import json
+import zipfile
 import copy
 import pyFAI
 from pyFAI.io import Nexus
@@ -78,6 +79,13 @@ def parse():
         help="extract every individual frame",
         default=False,
     )
+    parser.add_argument(
+        "-z",
+        "--zip",
+        action="store_true",
+        help="extract every individual frame into a zip-file",
+        default=False,
+    )
     return parser.parse_args()
 
 
@@ -87,11 +95,24 @@ def extract_averaged(filename):
     results["filename"] = filename
     # Missing: comment normalization
     with Nexus(filename, "r") as nxsr:
-        entry_grp = nxsr.get_entries()[0]
+        default = nxsr.h5.attrs.get("default")
+        if default and default in nxsr.h5:
+            entry_grp = nxsr.h5[default]
+        else:
+            entry_grp = nxsr.get_entries()[0]
         results["h5path"] = entry_grp.name
-        nxdata_grp = nxsr.h5[entry_grp.attrs["default"]]
+        # program = entry_grp.get("program_name")
+        # if program == ""
+        default = entry_grp.attrs["default"]
+        if posixpath.split(default)[-1] == "hplc":
+            default = posixpath.join(posixpath.split(default)[0],"results")
+        # print(default)
+        nxdata_grp = nxsr.h5[default]
         signal = nxdata_grp.attrs["signal"]
         axis = nxdata_grp.attrs["axes"]
+        if not isinstance(axis, (str,bytes)):
+            logger.error(f"There are several curves if the dataset {default} from file {filename}, please use the option --all to extract them all")
+            sys.exit(1)
         results["I"] = nxdata_grp[signal][()]
         results["q"] = nxdata_grp[axis][()]
         results["std"] = nxdata_grp["errors"][()]
@@ -102,15 +123,12 @@ def extract_averaged(filename):
         results["geometry"] = json.loads(
             integration_grp["configuration/data"][()]
         )
-        results["polarization"] = integration_grp[
-            "configuration/polarization_factor"
-        ][()]
+        results["polarization"] = integration_grp["configuration/polarization_factor"][()]
 
         instrument_grps = nxsr.get_class(entry_grp, class_type="NXinstrument")
         if instrument_grps:
-            detector_grp = nxsr.get_class(
-                instrument_grps[0], class_type="NXdetector"
-            )[0]
+            detector_grp = nxsr.get_class(instrument_grps[0], 
+                                          class_type="NXdetector")[0]
             results["mask"] = detector_grp["pixel_mask"].attrs["filename"]
         sample_grp = nxsr.get_class(entry_grp, class_type="NXsample")[0]
         results["sample"] = posixpath.split(sample_grp.name)[-1]
@@ -119,52 +137,68 @@ def extract_averaged(filename):
         results["exposure temperature"] = sample_grp["temperature"][()]
         results["concentration"] = sample_grp["concentration"][()]
         if "2_correlation_mapping" in entry_grp:
-            results["to_merge"] = entry_grp[
-                "2_correlation_mapping/results/to_merge"
-            ][()]
+            results["to_merge"] = entry_grp["2_correlation_mapping/results/to_merge"][()]
     return results
 
 
 def extract_all(filename):
-    "return some infomations extracted from a HDF5 file for  all individual frames"
+    """return some infomations extracted from a HDF5 file for all individual frames. 
+    Supports HPLC and SC and freshly integrated blocks of frames"""
     res = []
     results = OrderedDict()
     results["filename"] = filename
     with Nexus(filename, "r") as nxsr:
-        entry_grp = nxsr.get_entries()[0]
+        default = nxsr.h5.attrs.get("default")
+        if default and default in nxsr.h5:
+            entry_grp = nxsr.h5[default]
+        else:
+            entry_grp = nxsr.get_entries()[0]
+        program = entry_grp.get("program_name")[()].decode() if "program_name" in entry_grp else None
+
+        if program == "bm29.hplc":
+            target = "1_chromatogram"
+        elif program == "bm29.integratemultiframe":
+            target = "1_integration"
+        elif program == "bm29.subtract":
+            target = "3_azimuthal_integration"
+        else:
+            raise RuntimeError(f"Unable to read file written by {program}")
+        target = posixpath.join(entry_grp.name, target, "results")
         results["h5path"] = entry_grp.name
-        nxdata_grp = nxsr.h5[entry_grp.name + "/1_integration/results"]
+        nxdata_grp = nxsr.h5[target]
         signal = nxdata_grp.attrs["signal"]
         axis = nxdata_grp.attrs["axes"][1]
         I = nxdata_grp[signal][()]
         results["q"] = nxdata_grp[axis][()]
         std = nxdata_grp["errors"][()]
-        results["unit"] = pyFAI.units.to_unit(
-            axis + "_" + nxdata_grp[axis].attrs["units"]
-        )
+        try:
+            results["unit"] = pyFAI.units.to_unit(axis + "_" + nxdata_grp[axis].attrs["units"])
+        except KeyError:
+            logger.warning("Unable to parse radial units")
         integration_grp = nxdata_grp.parent
-        results["geometry"] = json.loads(
-            integration_grp["configuration/data"][()]
-        )
-        results["polarization"] = integration_grp[
-            "configuration/polarization_factor"
-        ][()]
-        instrument_grp = nxsr.get_class(entry_grp, class_type="NXinstrument")[
-            0
-        ]
-        detector_grp = nxsr.get_class(instrument_grp, class_type="NXdetector")[
-            0
-        ]
-        results["mask"] = detector_grp["pixel_mask"].attrs["filename"]
-        sample_grp = nxsr.get_class(entry_grp, class_type="NXsample")[0]
-        results["sample"] = posixpath.split(sample_grp.name)[-1]
-        results["buffer"] = sample_grp["buffer"][()]
-        if "temperature_env" in sample_grp:
-            results["storage temperature"] = sample_grp["temperature_env"][()]
-        if "temperature" in sample_grp:
-            results["exposure temperature"] = sample_grp["temperature"][()]
-        if "concentration" in sample_grp:
-            results["concentration"] = sample_grp["concentration"][()]
+        if "configuration/data" in integration_grp:
+            results["geometry"] = json.loads(integration_grp["configuration/data"][()])
+        else:
+            logger.warning("Unable to parse AzimuthalIntegrator configuration")
+        if "configuration/polarization_factor" in integration_grp:
+            results["polarization"] = integration_grp["configuration/polarization_factor"][()]
+        instrument_grp = nxsr.get_class(entry_grp, class_type="NXinstrument")
+        if instrument_grp:
+            detector_grp = nxsr.get_class(instrument_grp[0], class_type="NXdetector")
+            if detector_grp:
+                results["mask"] = detector_grp[0]["pixel_mask"].attrs["filename"]
+        sample_grp = nxsr.get_class(entry_grp, class_type="NXsample")
+        if sample_grp:
+            sample_grp = sample_grp[0]
+            results["sample"] = posixpath.split(sample_grp.name)[-1]
+            if "buffer" in sample_grp:
+                results["buffer"] = sample_grp["buffer"][()]
+            if "temperature_env" in sample_grp:
+                results["storage temperature"] = sample_grp["temperature_env"][()]
+            if "temperature" in sample_grp:
+                results["exposure temperature"] = sample_grp["temperature"][()]
+            if "concentration" in sample_grp:
+                results["concentration"] = sample_grp["concentration"][()]
     #         if "2_correlation_mapping" in entry_grp:
     #             results["to_merge"] = entry_grp["2_correlation_mapping/results/to_merge"][()]
     for i, s in zip(I, std):
@@ -326,15 +360,23 @@ def main():
     input_len = len(files)
     logger.debug("%s input files", input_len)
     for src in files:
+        print(f"{src} \t --> ", end="")
         if args.all:
             dest = os.path.splitext(src)[0] + "%04i.dat"
             for idx, frame in enumerate(extract_all(src)):
                 print(src, " --> ", dest % idx)
                 write_ascii(frame, dest % idx)
+            print(dest)
+        elif args.zip:
+            dest = os.path.splitext(src)[0] + ".zip"
+            with zipfile.ZipFile(dest, "w") as z:
+                for idx, frame in enumerate(extract_all(src)):
+                    z.writestr(f'frame_{idx:04d}.dat', write_ascii(frame))
+            print(dest)
         else:
             dest = os.path.splitext(src)[0] + ".dat"
             write_ascii(extract_averaged(src), dest)
-            print(src, " --> ", dest)
+            print(dest)
 
 
 if __name__ == "__main__":

src/freesas/meson.build

@@ -21,6 +21,7 @@ py.install_sources([
     'sasio.py',
     'transformations.py',
     'dnn.py',
+    'nexus_parser.py',
 ],
   pure: false,    # Will be installed next to binaries
   subdir: 'freesas'  # Folder relative to site-packages to install to

src/freesas/nexus_parser.py

@@ -0,0 +1,182 @@
+__author__ = "Jérôme Kieffer"
+__license__ = "MIT"
+__copyright__ = "2017, ESRF"
+__date__ = "20/01/2025"
+
+import sys, os
+import zipfile
+import posixpath
+import logging
+from typing import Union
+from silx.io.nxdata import NXdata
+from dataclasses import dataclass
+import numpy
+logger = logging.getLogger(__name__)
+
+try:
+    import h5py
+except ImportError:
+    logger.error("H5py is mandatory to parse HDF5 files")
+    h5py = None
+
+
+@dataclass
+class IntegratedPattern:
+    """Store one pyFAI integrated pattern"""
+
+    point: Union[float, int, None]
+    radial: numpy.ndarray
+    intensity: numpy.ndarray
+    intensity_errors: Union[numpy.ndarray, None]=None
+    radial_name: str = ""
+    radial_units: str = ""
+    intensity_name: str = ""
+    intensity_units: str = ""
+
+    def __repr__(self):
+        line = f"# {self.radial_name}({self.radial_units}) \t {self.intensity_name}({self.intensity_units})"
+        if self.intensity_errors is not None:
+            line += " \t uncertainties"
+        res = [line]
+        if self.intensity_errors is None:
+            for q,i,s in zip(self.radial, self.intensity):
+                res.append(f"{q} \t {i}")
+        else:
+            for q,i,s in zip(self.radial, self.intensity, self.intensity_errors):
+                res.append(f"{q} \t {i} \t {s}")
+        return os.linesep.join(res)
+
+
+def read_nexus_integrated_patterns(group):
+    """Read integrated patterns from a HDF5 NXdata group.
+
+    It reads from both single (1D signal) or multi (2D signal) NXdata.
+    :param group : h5py.Group
+    :return: list of IntegratedPattern instances.
+    """
+    nxdata = NXdata(group)
+    if not nxdata.is_valid:
+        raise RuntimeError(
+            f"Cannot parse NXdata group: {group.file.filename}::{group.name}"
+        )
+    if not (nxdata.signal_is_1d or nxdata.signal_is_2d):
+        raise RuntimeError(
+            f"Signal is not a 1D or 2D dataset: {group.file.filename}::{group.name}"
+        )
+
+    if nxdata.signal_is_1d:
+        points = [None]
+    else:  # 2d
+        if nxdata.axes[0] is None:
+            points = [None] * nxdata.signal.shape[0]
+        else:
+            points = nxdata.axes[0][()]
+
+    if nxdata.axes[-1] is None:
+        radial = numpy.arange(nxdata.signal.shape[1])
+        radial_units = ""
+        radial_name =  ""
+    else:
+        axis_dataset = nxdata.axes[-1]
+        radial = axis_dataset[()]
+        radial_name = axis_dataset.name.split("/")[-1]    
+        radial_units = axis_dataset.attrs.get("units", "")
+
+    intensities = numpy.atleast_2d(nxdata.signal)
+    intensity_name = nxdata.signal.name.split("/")[-1]
+    intensity_units = nxdata.signal.attrs.get("units", "")
+
+
+    if nxdata.errors is None:
+        errors = [None] * intensities.shape[0]
+    else:
+        errors = numpy.atleast_2d(nxdata.errors)
+
+    if (len(points), len(radial)) != intensities.shape:
+        raise RuntimeError("Shape mismatch between axes and signal")
+
+    return [IntegratedPattern(
+            point, radial, intensity, intensity_errors, radial_name, radial_units, intensity_name, intensity_units) for point, intensity, intensity_errors in zip(points, intensities, errors)]
+
+
+class Tree:
+    def __init__(self, root=None):
+        self.root = root or {}
+        self.skip = set()
+    def visit_item(self, name, obj):
+        if name in self.skip:
+                return
+        node = self.root
+        path = [i.replace(" ","_") for i in name.split("/")]
+        for i in path[:-1]:
+            if i not in node:
+                node[i] = {}
+            node = node[i]
+        if isinstance(obj, h5py.Group):
+            if obj.attrs.get("NX_class") == "NXdata" and "errors" in obj:
+                try:
+                    node[path[-1]] = read_nexus_integrated_patterns(obj)
+                except (KeyError, OSError) as err:
+                    print(f"{type(err).__name__}: {err} while readding {path}")
+                for key in obj:
+                    self.skip.add(posixpath.join(name,key))                    
+                    if isinstance(obj[key], h5py.Group):
+                        for sub in obj[key]:
+                            self.skip.add(posixpath.join(name,key, sub))
+            else:
+                node[path[-1]] = {}
+        if isinstance(obj, h5py.Dataset):
+            if len(obj.shape) <= 1:
+                node[path[-1]] = obj[()]
+
+    def save(self, filename):
+        with zipfile.ZipFile(filename, "w") as z:
+            def write(path, name, obj):
+                new_path = posixpath.join(path, name)
+                if isinstance(obj, dict):
+                    if sys.version_info>=(3,11): z.mkdir(new_path)
+                    for key, value in obj.items():
+                        write(new_path, key, value)
+                elif isinstance(obj, numpy.ndarray):
+                    if obj.ndim == 1:
+                        z.writestr(new_path, os.linesep.join(str(i) for i in obj))
+                    else:
+                        z.writestr(new_path, str(obj))      
+                elif isinstance(obj, list):
+                    if sys.version_info>=(3,11): z.mkdir(new_path)
+                    if len(obj)==1:
+                        fname = new_path+"/biosaxs.dat"
+                        z.writestr(fname, str(obj[0]))      
+                    else:
+                        for i,j in enumerate(obj):
+                            fname = new_path+f"/bioxaxs_{i:04d}.dat"
+                            z.writestr(fname, str(j))
+                elif isinstance(obj, (int, float, numpy.number, bool, numpy.bool)):
+                    z.writestr(new_path, str(obj))      
+                elif isinstance(obj, (str, bytes)):
+                    z.writestr(new_path, obj)      
+                else:
+                    print(f"skip {new_path} for {obj} of type {obj.__class__.__mro__}")
+
+            root = self.root
+            for key, value in root.items():
+                write("", key, value)
+    def get(self, path):
+        node = self.root
+        for i in path.split("/"):
+            node = node[i]
+        return node
+
+def convert_nexus2zip(nexusfile, outfile=None):
+    """ Convert a nexus-file, as produced by BM29 beamline into a zip file
+
+    :param nexusfile: string with the path of the input file
+    :param outfile: name of the output file, unless, just replace the extension with ".zip"
+    :return: nothing, maybe an error code ?
+    """
+    tree = Tree()
+    with h5py.File(nexusfile, "r") as h:
+        h.visititems(tree.visit_item)
+    outfile = outfile or (os.path.splitext(nexusfile)[0]+".h5")
+    tree.save(outfile)
+