diff --git a/e02/templates/ptyrex_basic.yaml b/e02/templates/ptyrex_basic.yaml index 0ff3228..7e47926 100644 --- a/e02/templates/ptyrex_basic.yaml +++ b/e02/templates/ptyrex_basic.yaml @@ -25,7 +25,7 @@ spec: volumes: - name: session hostPath: - path: "{{`{{ workflows.parameters.visitdir}}`}}" + path: "{{`{{ workflow.parameters.visitdir}}`}}" type: Directory volumeClaimTemplates: - metadata: @@ -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 @@ -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 @@ -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: