diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 9035d06..d1c4ccc 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -9,6 +9,6 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - - uses: pre-commit/action@v2.0.3 + - uses: actions/checkout@v4.3.0 + - uses: actions/setup-python@v5.6.0 + - uses: pre-commit/action@v3.0.1 diff --git a/.github/workflows/publish-ghcr.yml b/.github/workflows/publish-ghcr.yml new file mode 100644 index 0000000..401eeda --- /dev/null +++ b/.github/workflows/publish-ghcr.yml @@ -0,0 +1,59 @@ +# +name: Create and publish a Docker image + +# Configures this workflow to run every time a change is pushed to the branch called `release`. +on: + push: + branches: ['main'] + +# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds. +env: + REGISTRY: ghcr.io + IMAGE_NAME: ${{ github.repository }} + +# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu. +jobs: + build-and-push-image: + runs-on: ubuntu-latest + # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job. + permissions: + contents: read + packages: write + attestations: write + id-token: write + # + steps: + - name: Checkout repository + uses: actions/checkout@v5 + # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here. + - name: Log in to the Container registry + uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1 + with: + registry: ${{ env.REGISTRY }} + username: ${{ github.actor }} + password: ${{ secrets.GITHUB_TOKEN }} + # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels. + - name: Extract metadata (tags, labels) for Docker + id: meta + uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7 + with: + images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} + # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages. + # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see [Usage](https://github.com/docker/build-push-action#usage) in the README of the `docker/build-push-action` repository. + # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step. + - name: Build and push Docker image + id: push + uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4 + with: + context: . + push: true + tags: ${{ steps.meta.outputs.tags }} + labels: ${{ steps.meta.outputs.labels }} + + # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see [Using artifact attestations to establish provenance for builds](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds). + - name: Generate artifact attestation + uses: actions/attest-build-provenance@v3 + with: + subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}} + subject-digest: ${{ steps.push.outputs.digest }} + push-to-registry: true diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 64436ac..3a0db32 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -14,7 +14,7 @@ repos: - id: debug-statements - repo: https://github.com/timothycrosley/isort - rev: 5.9.3 + rev: 6.1.0 hooks: - id: isort diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..b4ac7e4 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,27 @@ +FROM ghcr.io/prefix-dev/pixi:latest + +ENV TZ="America/New_York" + +RUN apt-get -y update && \ + apt-get -y install git + +COPY pixi.toml . +COPY pixi.lock . +# use `--locked` to ensure the lockfile is up to date with pixi.toml +RUN pixi install --locked +# create the shell-hook bash script to activate the environment +RUN pixi shell-hook -s bash > /shell-hook + +ENV PYTHONUNBUFFERED=1 + +COPY test.py . + +RUN mkdir /etc/tiled +RUN mkdir /.prefect -m 0777 +RUN mkdir /repo -m 0777 + +RUN /bin/bash /shell-hook + +#now reapply deployment to push the image that is being created +ENTRYPOINT ["pixi", "run"] +CMD ["python", "-m", "test", "arg"] diff --git a/data_validation.py b/data_validation.py index dbc611b..9c068c7 100644 --- a/data_validation.py +++ b/data_validation.py @@ -1,18 +1,14 @@ import time from prefect import flow, get_run_logger, task -from tiled.client import from_profile - - -def initialize_tiled_client(): - return from_profile("nsls2") +from utils import get_tiled_client @task(retries=2, retry_delay_seconds=10) def read_all_streams(uid, beamline_acronym="haxpes"): logger = get_run_logger() - tiled_client = initialize_tiled_client() - run = tiled_client[beamline_acronym]["raw"][uid] + tiled_client = get_tiled_client() + run = tiled_client["raw"][uid] logger.info(f"Validating uid {run.start['uid']}") start_time = time.monotonic() for stream in run: diff --git a/end_of_run_workflow.py b/end_of_run_workflow.py index 0553a5d..09f59e1 100644 --- a/end_of_run_workflow.py +++ b/end_of_run_workflow.py @@ -1,9 +1,9 @@ from prefect import flow, get_run_logger, task from data_validation import general_data_validation - from general_exporter import export_switchboard + @task def log_completion(): logger = get_run_logger() diff --git a/export_tools.py b/export_tools.py index 4e58730..830dd14 100644 --- a/export_tools.py +++ b/export_tools.py @@ -1,10 +1,12 @@ -from numpy import column_stack, transpose, empty -from tiled.client import from_profile -import re +from numpy import column_stack, transpose +from utils import get_tiled_client + def get_proposal_path(run): proposal = run.start.get("proposal", {}).get("proposal_id", None) - is_commissioning = "commissioning" in run.start.get("proposal", {}).get("type", "").lower() + is_commissioning = ( + "commissioning" in run.start.get("proposal", {}).get("type", "").lower() + ) cycle = run.start.get("cycle", None) if proposal is None or cycle is None: raise ValueError("Proposal Metadata not Loaded") @@ -14,18 +16,21 @@ def get_proposal_path(run): proposal_path = f"/nsls2/data/sst/proposals/{cycle}/pass-{proposal}/" return proposal_path + def get_ses_path(run): base_path = get_proposal_path(run) - ses_path = base_path+"assets/haxpes-ses/" + ses_path = base_path + "assets/haxpes-ses/" return ses_path -def get_md(run,md_key,default="Unknown"): + +def get_md(run, md_key, default="Unknown"): if md_key in run.start.keys(): return str(run.start[md_key]) else: return default -def get_baseline(run,md_key,default="Unknown",firstonly=False): + +def get_baseline(run, md_key, default="Unknown", firstonly=False): if md_key in run.baseline.data.keys(): if firstonly: return str(run.baseline.data[md_key].read()[0]) @@ -34,79 +39,82 @@ def get_baseline(run,md_key,default="Unknown",firstonly=False): else: return default -def get_baseline_config(run,device,md_key,default="Unknown"): - fullkey = str(device+"_"+md_key) + +def get_baseline_config(run, device, md_key, default="Unknown"): + fullkey = str(device + "_" + md_key) if fullkey in run.baseline.config[device].keys(): return str(run.baseline.config[device][fullkey].read()[0]) else: return default -def get_photon_energy(run,default=0): - if 'beam_selection' in run.baseline.data.keys(): - beamselect = run.baseline.data['beam_selection'].read()[0] + +def get_photon_energy(run, default=0): + if "beam_selection" in run.baseline.data.keys(): + beamselect = run.baseline.data["beam_selection"].read()[0] if beamselect == "Tender": - en = round(run.baseline.data['SST2 Energy_energy'].read().mean(),1) + en = round(run.baseline.data["SST2 Energy_energy"].read().mean(), 1) elif beamselect == "Soft": - en = round(run.baseline.data['en_energy'].read().mean(),1) + en = round(run.baseline.data["en_energy"].read().mean(), 1) else: en = default else: en = default return str(en) - + def get_scantype(run): if "scantype" in run.start.keys(): - return run.start['scantype'] + return run.start["scantype"] else: - return None + return None + def get_general_metadata(run): metadata = get_mono_md(run) - + try: - metadata['Proposal'] = str(run.start['proposal']['proposal_id']) - except: - metadata['Proposal'] = unknown - - metadata['UID'] = get_md(run,'uid') - metadata['Start Date/Time'] = get_md(run,'start_datetime') - metadata['Scan ID'] = get_md(run,'scan_id') - metadata['SAF'] = get_md(run,'saf') - metadata['Sample Name'] = get_md(run,'sample_name') - metadata['Sample Description'] = get_md(run,'sample_desc') -# metadata['Mono Crystal'] = get_baseline_config(run,'SST2 Energy','mono_crystal') -# metadata['Undulator Harmonic'] = get_baseline_config(run,'SST2 Energy','harmonic') - metadata['Comment'] = get_md(run,'comment') - - if len(run.start['hints']['dimensions']) == 1: - if len(run.start['hints']['dimensions'][0][0]) == 1: - x_key = run.start['hints']['dimensions'][0][0][0] + metadata["Proposal"] = str(run.start["proposal"]["proposal_id"]) + except: + metadata["Proposal"] = unknown + + metadata["UID"] = get_md(run, "uid") + metadata["Start Date/Time"] = get_md(run, "start_datetime") + metadata["Scan ID"] = get_md(run, "scan_id") + metadata["SAF"] = get_md(run, "saf") + metadata["Sample Name"] = get_md(run, "sample_name") + metadata["Sample Description"] = get_md(run, "sample_desc") + # metadata['Mono Crystal'] = get_baseline_config(run,'SST2 Energy','mono_crystal') + # metadata['Undulator Harmonic'] = get_baseline_config(run,'SST2 Energy','harmonic') + metadata["Comment"] = get_md(run, "comment") + + if len(run.start["hints"]["dimensions"]) == 1: + if len(run.start["hints"]["dimensions"][0][0]) == 1: + x_key = run.start["hints"]["dimensions"][0][0][0] else: x_key = "I dunno" - metadata['X Label'] = x_key + metadata["X Label"] = x_key - metadata['Detectors'] = get_md(run,'detectors') + metadata["Detectors"] = get_md(run, "detectors") - metadata['FloodGun Energy'] = get_baseline_config(run,'FloodGun','energy') - metadata['FloodGun Emission'] = get_baseline_config(run,'FloodGun','Iemis') - metadata['FloodGun Grid Voltage'] = get_baseline_config(run,'FloodGun','Vgrid') - - metadata['L1 Stripe'] = get_baseline(run,'L1_stripe',firstonly=True) - metadata['L2 Mirror'] = get_baseline(run,'L2_mirror_type',firstonly=True) - metadata['L2 Stripe'] = get_baseline(run,'L2_stripe',firstonly=True) + metadata["FloodGun Energy"] = get_baseline_config(run, "FloodGun", "energy") + metadata["FloodGun Emission"] = get_baseline_config(run, "FloodGun", "Iemis") + metadata["FloodGun Grid Voltage"] = get_baseline_config(run, "FloodGun", "Vgrid") - metadata['HSlit Gap'] = get_baseline(run,'HAXPES slits_hsize') - metadata['HSlit Center'] = get_baseline(run,'HAXPES slits_hcenter') - metadata['VSlit Gap'] = get_baseline(run,'HAXPES slits_vsize') - metadata['VSlit Center'] = get_baseline(run,'HAXPES slits_vcenter') - metadata['Sample X'] = get_baseline(run,'haxpes_manipulator_x') - metadata['Sample Y'] = get_baseline(run,'haxpes_manipulator_y') - metadata['Sample Z'] = get_baseline(run,'haxpes_manipulator_z') - metadata['Sample Rotation'] = get_baseline(run,'haxpes_manipulator_r') + metadata["L1 Stripe"] = get_baseline(run, "L1_stripe", firstonly=True) + metadata["L2 Mirror"] = get_baseline(run, "L2_mirror_type", firstonly=True) + metadata["L2 Stripe"] = get_baseline(run, "L2_stripe", firstonly=True) - return metadata + metadata["HSlit Gap"] = get_baseline(run, "HAXPES slits_hsize") + metadata["HSlit Center"] = get_baseline(run, "HAXPES slits_hcenter") + metadata["VSlit Gap"] = get_baseline(run, "HAXPES slits_vsize") + metadata["VSlit Center"] = get_baseline(run, "HAXPES slits_vcenter") + metadata["Sample X"] = get_baseline(run, "haxpes_manipulator_x") + metadata["Sample Y"] = get_baseline(run, "haxpes_manipulator_y") + metadata["Sample Z"] = get_baseline(run, "haxpes_manipulator_z") + metadata["Sample Rotation"] = get_baseline(run, "haxpes_manipulator_r") + + return metadata def get_metadata_xps(run): @@ -114,38 +122,46 @@ def get_metadata_xps(run): metadata = get_general_metadata(run) try: - peak_config = run.primary.descriptors[0]['configuration']['PeakAnalyzer']['data'] + peak_config = run.primary.descriptors[0]["configuration"]["PeakAnalyzer"][ + "data" + ] for peakkey in peak_config.keys(): - out_key = peakkey.replace("_"," ") + out_key = peakkey.replace("_", " ") metadata[out_key] = str(peak_config[peakkey]) except KeyError: - metadata['Peak Analyzer'] = "Not Used" + metadata["Peak Analyzer"] = "Not Used" - metadata['I0 Integration Time'] = str(run.primary.descriptors[0]['configuration']['I0 ADC']['data']['I0 ADC_exposure_time']) - metadata['I0 Data'] = str(run.primary.read()["I0 ADC"].data) + metadata["I0 Integration Time"] = str( + run.primary.descriptors[0]["configuration"]["I0 ADC"]["data"][ + "I0 ADC_exposure_time" + ] + ) + metadata["I0 Data"] = str(run.primary.read()["I0 ADC"].data) - metadata['Excitation Energy'] = get_photon_energy(run) + metadata["Excitation Energy"] = get_photon_energy(run) - metadata['Number of Sweeps'] = get_md(run,'sweeps') + metadata["Number of Sweeps"] = get_md(run, "sweeps") return metadata + def get_data_xps(run): - energy_axis = run.primary.read()["PeakAnalyzer_xaxis"].data[0,:] - imdat = run.primary.read()['PeakAnalyzer_edc'].data + energy_axis = run.primary.read()["PeakAnalyzer_xaxis"].data[0, :] + imdat = run.primary.read()["PeakAnalyzer_edc"].data - #add dimension mode should be a metadata key. If true, keep every sweep individually. For now force False + # add dimension mode should be a metadata key. If true, keep every sweep individually. For now force False add_dimension = False if add_dimension: edc = transpose(imdat) else: edc = imdat.sum(axis=0) - data_array = column_stack((energy_axis,edc)) + data_array = column_stack((energy_axis, edc)) return data_array + def get_mono_md(run): """ checks if SST-1 or SST-2, then gets correct md. @@ -153,133 +169,150 @@ def get_mono_md(run): """ metadata = {} - if 'beam_selection' in run.baseline.data.keys(): - beamselect = run.baseline.data['beam_selection'].read()[0] + if "beam_selection" in run.baseline.data.keys(): + beamselect = run.baseline.data["beam_selection"].read()[0] if beamselect == "Tender": - metadata['Mono Crystal'] = get_baseline_config(run,'SST2 Energy','mono_crystal') - metadata['Undulator Harmonic'] = get_baseline_config(run,'SST2 Energy','harmonic') - metadata['Filter Position'] = get_baseline(run,'nBPM Filter') + metadata["Mono Crystal"] = get_baseline_config( + run, "SST2 Energy", "mono_crystal" + ) + metadata["Undulator Harmonic"] = get_baseline_config( + run, "SST2 Energy", "harmonic" + ) + metadata["Filter Position"] = get_baseline(run, "nBPM Filter") elif beamselect == "Soft": - metadata['CFF'] = get_baseline_config(run,'en','monoen_cff') - metadata['Grating'] = get_baseline_config(run,'en','monoen_gratingx_setpoint') - metadata['Mirror2'] = get_baseline_config(run,'en','monoen_mirror2x_setpoint') - metadata['Undulator Harmonic'] = get_baseline_config(run,'en','harmonic') - metadata['Exit Slit Gap'] = get_baseline(run,'Exit Slit AB') + metadata["CFF"] = get_baseline_config(run, "en", "monoen_cff") + metadata["Grating"] = get_baseline_config( + run, "en", "monoen_gratingx_setpoint" + ) + metadata["Mirror2"] = get_baseline_config( + run, "en", "monoen_mirror2x_setpoint" + ) + metadata["Undulator Harmonic"] = get_baseline_config(run, "en", "harmonic") + metadata["Exit Slit Gap"] = get_baseline(run, "Exit Slit AB") return metadata -def make_header(metadata,datatype,detlist=None): + +def make_header(metadata, datatype, detlist=None): """ compiles metadata into a header for data export. Datatype should be "xps" or "xas" """ header = "" - for k in metadata.keys(): - header = header + k + ": "+metadata[k]+"\n" + for k in metadata.keys(): + header = header + k + ": " + metadata[k] + "\n" if datatype == "xps": - header = header+'\n' - header = header+'[Data]\n' - header = header+'Energy' - for n in range(int(metadata['Number of Sweeps'])): - header = header+", Dimension"+str(n) - header = header+"\n" + header = header + "\n" + header = header + "[Data]\n" + header = header + "Energy" + for n in range(int(metadata["Number of Sweeps"])): + header = header + ", Dimension" + str(n) + header = header + "\n" elif datatype == "xas": - header = header+'\n' - header = header+'-----------------------------------------\n' - header = header+'Energy' + header = header + "\n" + header = header + "-----------------------------------------\n" + header = header + "Energy" if detlist != None: for det in detlist: - header = header+", "+det.replace(" ","_") - header = header+"\n" + header = header + ", " + det.replace(" ", "_") + header = header + "\n" elif datatype == "generic": - header = header+"\n" - header = header+'-----------------------------------------\n' - header = header+metadata['X Label'].replace(" ","_") + header = header + "\n" + header = header + "-----------------------------------------\n" + header = header + metadata["X Label"].replace(" ", "_") if detlist != None: for det in detlist: - header = header+", "+det.replace(" ","_") - header = header+"\n" - + header = header + ", " + det.replace(" ", "_") + header = header + "\n" + else: pass - + return header -def write_header_only(fpath,header): - fobj = open(fpath,'w') + +def write_header_only(fpath, header): + fobj = open(fpath, "w") fobj.write(header) fobj.close() + def get_xas_data(run): - data_array = run.primary.read()['SST2 Energy_energy'].data + data_array = run.primary.read()["SST2 Energy_energy"].data - detlist = run.start['detectors'] + detlist = run.start["detectors"] for det in detlist: if det == "PeakAnalyzer": - data_array = column_stack((data_array,run.primary.read()['PeakAnalyzer_total_counts'].data)) + data_array = column_stack( + (data_array, run.primary.read()["PeakAnalyzer_total_counts"].data) + ) else: - data_array = column_stack((data_array,run.primary.read()[det].data)) + data_array = column_stack((data_array, run.primary.read()[det].data)) return data_array + def get_generic_1d_data(run): - if len(run.start['hints']['dimensions']) == 1: - if len(run.start['hints']['dimensions'][0][0]) == 1: - x_key = run.start['hints']['dimensions'][0][0][0] + if len(run.start["hints"]["dimensions"]) == 1: + if len(run.start["hints"]["dimensions"][0][0]) == 1: + x_key = run.start["hints"]["dimensions"][0][0][0] else: - return #I don't know what to do - + return # I don't know what to do + data_array = run.primary.read()[x_key].data - detlist = run.start['detectors'] + detlist = run.start["detectors"] for det in detlist: if det == "PeakAnalyzer": - data_array = column_stack((data_array,run.primary.read()['PeakAnalyzer_total_counts'].data)) + data_array = column_stack( + (data_array, run.primary.read()["PeakAnalyzer_total_counts"].data) + ) else: - data_array = column_stack((data_array,run.primary.read()[det].data)) + data_array = column_stack((data_array, run.primary.read()[det].data)) return data_array def initialize_tiled_client(beamline_acronym): - return from_profile("nsls2")[beamline_acronym]['raw'] + return get_tiled_client()["raw"] + -def generate_file_name(run,extension): - """ generates a file name from the metadata in the run. +def generate_file_name(run, extension): + """generates a file name from the metadata in the run. If no export filename or sample name is given, filename will be Scan_. """ S = "" - if 'export_filename' in run.start.keys() and run.start['export_filename']: - S = S+run.start['export_filename'] - elif 'sample_name' in run.start.keys(): - S = S+run.start['sample_name'] + if "export_filename" in run.start.keys() and run.start["export_filename"]: + S = S + run.start["export_filename"] + elif "sample_name" in run.start.keys(): + S = S + run.start["sample_name"] S = sanitize_filename(S) if S == "": S = "Scan" - #would be nice to have photon energy for XPS, but don't know how to make that work for both soft and tender yet - N = run.start['scan_id'] + # would be nice to have photon energy for XPS, but don't know how to make that work for both soft and tender yet + N = run.start["scan_id"] - if 'scantype' in run.start.keys() and run.start['scantype'] == "xps": + if "scantype" in run.start.keys() and run.start["scantype"] == "xps": EC = "_" en = get_photon_energy(run) if en != "0": - EC = EC+f"{en}eV_" - cl = get_md(run,'core_line') + EC = EC + f"{en}eV_" + cl = get_md(run, "core_line") if cl != "Unknown": - EC = EC+f"{cl}" - elif 'scantype' in run.start.keys() and run.start['scantype'] == "xas": - cl = get_md(run,'edge') + EC = EC + f"{cl}" + elif "scantype" in run.start.keys() and run.start["scantype"] == "xas": + cl = get_md(run, "edge") EC = f"_{cl}" else: EC = "" - if extension[0] == ".": extension = extension[1:] fn = f"{S}{EC}_{N}.{extension}" return fn - + + def sanitize_filename(filename): """ Sanitize a filename by removing/replacing invalid characters. Avoids wrecking @@ -307,81 +340,82 @@ def sanitize_filename(filename): filename = re.sub(r"[_\s]+", "_", filename) return filename + def get_resPES_data(run): data_dictionary = {} - + metadata = get_general_metadata(run) try: - peak_config = run.primary.descriptors[0]['configuration']['PeakAnalyzer']['data'] + peak_config = run.primary.descriptors[0]["configuration"]["PeakAnalyzer"][ + "data" + ] for peakkey in peak_config.keys(): - out_key = peakkey.replace("_"," ") + out_key = peakkey.replace("_", " ") metadata[out_key] = str(peak_config[peakkey]) except KeyError: - metadata['Peak Analyzer'] = "Not Used" - metadata['I0 Integration Time'] = str(run.primary.descriptors[0]['configuration']['I0 ADC']['data']['I0 ADC_exposure_time']) + metadata["Peak Analyzer"] = "Not Used" + metadata["I0 Integration Time"] = str( + run.primary.descriptors[0]["configuration"]["I0 ADC"]["data"][ + "I0 ADC_exposure_time" + ] + ) data_dictionary["Metadata"] = metadata - if 'shape' not in run.start.keys(): - return data_dictionary #just give up ... - if 'PeakAnalyzer' not in run.start['detectors']: - return data_dictionary #like I said ... + if "shape" not in run.start.keys(): + return data_dictionary # just give up ... + if "PeakAnalyzer" not in run.start["detectors"]: + return data_dictionary # like I said ... - beam_type = run.baseline.config['beam_selection']['beam_selection'].read()[0] + beam_type = run.baseline.config["beam_selection"]["beam_selection"].read()[0] if beam_type == "Tender": en_key = "SST2 Energy_energy" elif beam_type == "Soft": - en_key = "en_energy" ### check this !!! + en_key = "en_energy" ### check this !!! else: - return data_dictionary #again, just give up ... + return data_dictionary # again, just give up ... - n_hv = run.start['shape'][0] - n_sweep = run.start['shape'][1] + n_hv = run.start["shape"][0] + n_sweep = run.start["shape"][1] - n_KE = run.primary.read()['PeakAnalyzer_xaxis'].data.shape[1] + n_KE = run.primary.read()["PeakAnalyzer_xaxis"].data.shape[1] - hv = run.primary.read()[en_key].data.reshape(n_hv,n_sweep) + hv = run.primary.read()[en_key].data.reshape(n_hv, n_sweep) hv = hv.mean(axis=1) - sweep = run.primary.read()['Exposure'].data.reshape(n_hv,n_sweep) #check motor name + sweep = run.primary.read()["Exposure"].data.reshape( + n_hv, n_sweep + ) # check motor name sweep = sweep.mean(axis=0) - KE = run.primary.read()['PeakAnalyzer_xaxis'].data.reshape(n_hv,n_sweep,n_KE) - KE = KE.mean(axis=(0,1)) + KE = run.primary.read()["PeakAnalyzer_xaxis"].data.reshape(n_hv, n_sweep, n_KE) + KE = KE.mean(axis=(0, 1)) - edc = run.primary.read()['PeakAnalyzer_edc'].data.reshape(n_hv,n_sweep,n_KE) + edc = run.primary.read()["PeakAnalyzer_edc"].data.reshape(n_hv, n_sweep, n_KE) edc = edc.mean(axis=1) edc_norm = empty(edc.shape) for n in range(n_hv): - edc_norm[n,:] = edc[n,:] / edc[n,-20:].mean() + edc_norm[n, :] = edc[n, :] / edc[n, -20:].mean() - DataSets = { - 'edc_raw': edc, - 'edc_norm': edc_norm - } + DataSets = {"edc_raw": edc, "edc_norm": edc_norm} data_dictionary["DataSets"] = DataSets signals = {} - for det in run.start['detectors']: - if det != 'PeakAnalyzer': - detdat = run.primary.read()[det].data.reshape(n_hv,n_sweep) + for det in run.start["detectors"]: + if det != "PeakAnalyzer": + detdat = run.primary.read()[det].data.reshape(n_hv, n_sweep) detdat = detdat.mean(axis=1) signals[det] = detdat - AEY = run.primary.read()['PeakAnalyzer_total_counts'].data.reshape(n_hv,n_sweep) + AEY = run.primary.read()["PeakAnalyzer_total_counts"].data.reshape(n_hv, n_sweep) AEY = AEY.mean(axis=1) signals["AugerYield"] = AEY data_dictionary["Signals"] = signals - axes = { - "Photon Energy": hv, - "Kinetic Energy": KE - } + axes = {"Photon Energy": hv, "Kinetic Energy": KE} data_dictionary["Axes"] = axes return data_dictionary - - diff --git a/file_exporter.py b/file_exporter.py index 1ccdac6..037fa7e 100644 --- a/file_exporter.py +++ b/file_exporter.py @@ -1,74 +1,79 @@ -from export_tools import * -import numpy as np -from os import makedirs -from os.path import exists, splitext import shutil from glob import glob -import h5py +from os import makedirs +from os.path import exists, splitext + +import numpy as np + +from export_tools import * + def export_peak_xps(uid, beamline_acronym="haxpes"): catalog = initialize_tiled_client(beamline_acronym) run = catalog[uid] - metadata = get_metadata_xps(run) - header = make_header(metadata,"xps") + metadata = get_metadata_xps(run) + header = make_header(metadata, "xps") data = get_data_xps(run) - export_path = get_proposal_path(run)+"XPS_export/" + export_path = get_proposal_path(run) + "XPS_export/" if not exists(export_path): makedirs(export_path) - filename = export_path+generate_file_name(run,'csv') - np.savetxt(filename,data,delimiter=',',header=header) - + filename = export_path + generate_file_name(run, "csv") + np.savetxt(filename, data, delimiter=",", header=header) + + def export_ses_xps(uid, beamline_acronym="haxpes"): catalog = initialize_tiled_client(beamline_acronym) run = catalog[uid] metadata = get_metadata_xps(run) - header = make_header(metadata,"xps") - export_path = get_proposal_path(run)+"XPS_export/" + header = make_header(metadata, "xps") + export_path = get_proposal_path(run) + "XPS_export/" ses_path = get_ses_path(run) - scan_id = run.start['scan_id'] + scan_id = run.start["scan_id"] if not exists(export_path): makedirs(export_path) - filename = generate_file_name(run,'md') - out_path = export_path+filename - write_header_only(out_path,header) + filename = generate_file_name(run, "md") + out_path = export_path + filename + write_header_only(out_path, header) ses_files = glob(f"{ses_path}*_{scan_id}_*") for ses_file in ses_files: ext = splitext(ses_file)[1] - out_path = export_path+generate_file_name(run,ext) - shutil.copy(ses_file,out_path) + out_path = export_path + generate_file_name(run, ext) + shutil.copy(ses_file, out_path) def export_xas(uid, beamline_acronym="haxpes"): catalog = initialize_tiled_client(beamline_acronym) run = catalog[uid] - detlist = run.start['detectors'] - metadata = get_general_metadata(run) - header = make_header(metadata,"xas",detlist=detlist) + detlist = run.start["detectors"] + metadata = get_general_metadata(run) + header = make_header(metadata, "xas", detlist=detlist) data = get_xas_data(run) - export_path = get_proposal_path(run)+"XAS_export/" + export_path = get_proposal_path(run) + "XAS_export/" if not exists(export_path): makedirs(export_path) - filename = export_path+generate_file_name(run,'csv') - np.savetxt(filename,data,delimiter=',',header=header) + filename = export_path + generate_file_name(run, "csv") + np.savetxt(filename, data, delimiter=",", header=header) + def export_generic_1D(uid, beamline_acronym="haxpes"): catalog = initialize_tiled_client(beamline_acronym) run = catalog[uid] - detlist = run.start['detectors'] + detlist = run.start["detectors"] metadata = get_general_metadata(run) - header = make_header(metadata,"generic",detlist=detlist) + header = make_header(metadata, "generic", detlist=detlist) data = get_generic_1d_data(run) - export_path = get_proposal_path(run)+"GeneralExport/" + export_path = get_proposal_path(run) + "GeneralExport/" if not exists(export_path): makedirs(export_path) - filename = export_path+generate_file_name(run,'csv') - np.savetxt(filename,data,delimiter=',',header=header) + filename = export_path + generate_file_name(run, "csv") + np.savetxt(filename, data, delimiter=",", header=header) + def export_resPES(uid, beamline_acronym="haxpes"): catalog = initialize_tiled_client(beamline_acronym) @@ -76,25 +81,25 @@ def export_resPES(uid, beamline_acronym="haxpes"): data_dictionary = get_resPES_data(run) - export_path = get_proposal_path(run)+"ResPES/" + export_path = get_proposal_path(run) + "ResPES/" if not exists(export_path): makedirs(export_path) - filename = export_path+generate_file_name(run,'h5') - - f = h5py.File(filename,'a') + filename = export_path + generate_file_name(run, "h5") + + f = h5py.File(filename, "a") datagroup = f.create_group("DataSets") for key, value in data_dictionary["DataSets"].items(): - ds = datagroup.create_dataset(key,data=value) + ds = datagroup.create_dataset(key, data=value) specgroup = f.create_group("Signals") for key, value in data_dictionary["Signals"].items(): - s = specgroup.create_dataset(key,data=value) - s.attrs['X Axis'] = "Photon Energy" + s = specgroup.create_dataset(key, data=value) + s.attrs["X Axis"] = "Photon Energy" axisgroup = f.create_group("PlotAxes") for key, value in data_dictionary["Axes"].items(): - a = axisgroup.create_dataset(key,data=value) + a = axisgroup.create_dataset(key, data=value) metagroup = f.create_group("Meta") for key, value in data_dictionary["Metadata"].items(): diff --git a/general_exporter.py b/general_exporter.py index d4d0901..1b61efc 100644 --- a/general_exporter.py +++ b/general_exporter.py @@ -1,50 +1,57 @@ -from file_exporter import ( - export_xas, - export_peak_xps, - export_generic_1D, - export_ses_xps, - export_resPES - ) -#from export_tools import get_proposal_path +# from export_tools import get_proposal_path from prefect import flow + from export_tools import initialize_tiled_client +from file_exporter import ( + export_generic_1D, + export_peak_xps, + export_resPES, + export_ses_xps, + export_xas, +) -def export_switchboard(uid,beamline_acronym="haxpes"): + +def export_switchboard(uid, beamline_acronym="haxpes"): c = initialize_tiled_client(beamline_acronym) run = c[uid] - if run.stop['exit_status'] != "abort": - if run.start['autoexport']: - if 'scantype' in run.start.keys(): - if run.start['scantype'] == "xps": - if run.start['analyzer_type'] == "peak": + if run.stop["exit_status"] != "abort": + if run.start["autoexport"]: + if "scantype" in run.start.keys(): + if run.start["scantype"] == "xps": + if run.start["analyzer_type"] == "peak": peak_export(uid) - elif run.start['analyzer_type'] == "ses": + elif run.start["analyzer_type"] == "ses": ses_export(uid) - elif run.start['scantype'] == "xas": + elif run.start["scantype"] == "xas": xas_export(uid) - elif run.start['scantype'] == "resPES": + elif run.start["scantype"] == "resPES": resPES_export(uid) else: generic_export(uid) else: generic_export(uid) + @flow def xas_export(uid, beamline_acronym="haxpes"): - export_xas(uid,beamline_acronym) + export_xas(uid, beamline_acronym) + @flow def peak_export(uid, beamline_acronym="haxpes"): export_peak_xps(uid, beamline_acronym) + @flow def generic_export(uid, beamline_acronym="haxpes"): export_generic_1D(uid, beamline_acronym) + @flow -def ses_export(uid,beamline_acronym="haxpes"): +def ses_export(uid, beamline_acronym="haxpes"): export_ses_xps(uid, beamline_acronym) -@flow -def resPES_export(uid,beamline_acronym = "haxpes"): + +@flow +def resPES_export(uid, beamline_acronym="haxpes"): export_resPES(uid, beamline_acronym) diff --git a/pixi.lock b/pixi.lock new file mode 100644 index 0000000..cd4ee75 --- /dev/null +++ b/pixi.lock @@ -0,0 +1,6072 @@ +version: 6 +environments: + default: + channels: + - 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prefect.deployments.steps.set_working_directory: + directory: /repo - prefect.deployments.steps.git_clone: - repository: https://github.com/NSLS-II-SST/workflows-haxpes.git + repository: https://github.com/nsls2/haxpes-workflows.git branch: main - access_token: # the deployments section allows you to provide configuration for deploying flows deployments: - - name: haxpes-end-of-run-workflow - version: + - name: haxpes-end-of-run-workflow-docker + version: 0.1.1 tags: [haxpes] - description: - schedule: {} + description: Deploy the updated Docker image entrypoint: end_of_run_workflow.py:end_of_run_workflow parameters: {} work_pool: - name: haxpes-work-pool + name: haxpes-work-pool-docker work_queue_name: - job_variables: {} \ No newline at end of file + job_variables: + env: + TILED_SITE_PROFILES: /nsls2/software/etc/tiled/profiles + image: ghcr.io/nsls2/haxpes-workflows:main + image_pull_policy: Always + network: slirp4netns + volumes: + - /nsls2/data/sst/proposals:/nsls2/data/sst/proposals + - /nsls2/software/etc/tiled:/nsls2/software/etc/tiled + container_create_kwargs: + userns_mode: "keep-id:uid=402953,gid=402953" # workflow-sst:workflow-sst + auto_remove: true diff --git a/pyproject.toml b/pyproject.toml deleted file mode 100644 index 766a8c4..0000000 --- a/pyproject.toml +++ /dev/null @@ -1,9 +0,0 @@ -[tool.black] -line-length = 120 -exclude = ''' -( - /( - | \.git - )/ -) -''' diff --git a/test.py b/test.py new file mode 100644 index 0000000..e54521c --- /dev/null +++ b/test.py @@ -0,0 +1,17 @@ +from __future__ import annotations + +import sys + + +def test(stuff=""): + if stuff: + print(f"test: {stuff}") # noqa: T201 + else: + print("test: EMPTY") # noqa: T201 + + +if __name__ == "__main__": + if len(sys.argv) > 1: + test(sys.argv[1]) + else: + test() diff --git a/utils.py b/utils.py new file mode 100644 index 0000000..769e29a --- /dev/null +++ b/utils.py @@ -0,0 +1,12 @@ +from tiled.client import from_profile +from prefect.blocks.system import Secret + +import os + +LOCATION="haxpes" + +def get_tiled_client(): + os.environ["TILED_API_KEY"] = Secret.load(f"tiled-{LOCATION}-api-key", _sync=True).get() + tiled_client = from_profile("nsls2")[LOCATION] + os.environ.pop("TILED_API_KEY") + return tiled_client