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16 changes: 8 additions & 8 deletions e02/templates/ptyrex_basic.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ spec:
volumes:
- name: session
hostPath:
path: "{{`{{ workflows.parameters.visitdir}}`}}"
path: "{{`{{ workflow.parameters.visitdir}}`}}"
type: Directory
volumeClaimTemplates:
- metadata:
Expand Down Expand Up @@ -137,7 +137,7 @@ spec:
- name: ptyrex-probe-phase
path: /tmp/probe_phase.jpeg
archive:
none: {}
none: { }
script:
image: gitlab.diamond.ac.uk:5050/scisoft/ptychography/dimtools/mib2x
imagePullPolicy: Always
Expand All @@ -146,12 +146,7 @@ spec:
value: "{{ `{{inputs.parameters.nprocs}}` }}"
- name: OMP_NUM_THREADS
value: "{{ `{{inputs.parameters.nprocs}}` }}"
volumeMounts:
- name: tmpdir
mountPath: /tmp
- name: session
mountPath: "{{ `{{workflow.parameters.visitdir}}` }}"
command: [python]
command: [/bin/python]
source: |
#Aim: find the ptyrex_recon file and then load corresponding hdf file and
#create a jpeg of object/probe phase/modulus and display as artifacts
Expand Down Expand Up @@ -221,6 +216,11 @@ spec:
probe_mj.save(probe_modulus_path)
probe_pj = Image.fromarray(probe_ang)
probe_pj.save(probe_phase_path)
volumeMounts:
- name: tmpdir
mountPath: /tmp
- name: session
mountPath: "{{ `{{workflow.parameters.visitdir}}` }}"

podSpecPatch: |
containers:
Expand Down
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