Add general madym_T1 wrapper (set to IR_E by default)

config/madym_T1.config.yaml

@@ -0,0 +1,16 @@
+# madym_T1
+# version = v4.23.0
+
+method: IR_E
+
+T1_dir: IR
+T1_vols: [OE_400, OE_800, OE_1000, OE_1500, OE_2000, OE_2500]
+B1_name: null
+
+output_dir: T1_IR
+log_file: logs/madym_T1_IR.log
+config_out: logs/madym_T1_IR.conf
+
+T1_noise: 0.1
+B1_scaling: 1000
+B1_values: []

workflow/Snakefile

@@ -17,7 +17,7 @@ include: "rules/common.smk"
 # include: "rules/OE_deltaR1.smk"
 
 include: "rules/DCE_deltaCt.smk"
-
+include: "rules/madym_T1.smk"
 # include: "rules/DCE_ETM.smk"
 # # include: "rules/OE_DCE_hypoxia_mapping.smk"
 
@@ -26,7 +26,5 @@ include: "rules/DCE_deltaCt.smk"
 
 rule all:
     input:
-        expand("{maps_dir}/{key}{ext}",
-            maps_dir = data_path("maps_dir"),
-            key = ['C_t', 'delta_C', 'C_baseline', 'C_enhancing', 'C_p_vals', 'S_p_vals'],
-            ext = ".nii.gz"),
+        rules.DCE_deltaCt.output,
+        rules.madym_T1.output

workflow/rules/madym_T1.smk

@@ -0,0 +1,36 @@
+'''
+Wrapper for madym_T1
+'''
+import os
+from snakemake.utils import validate
+
+configfile: workflow.source_path("../../config/madym_T1.config.yaml")
+validate(config, workflow.source_path("../schemas/madym_T1.schema.yaml"))
+
+envvars:
+    "MADYM_ROOT"
+
+rule madym_T1:
+    container:
+        "docker://registry.gitlab.com/manchester_qbi/manchester_qbi_public/madym_cxx/madym_release_no_gui:u22.04"
+       # "preclinicalmri_depends_no_gui:latest"
+    input:
+        # TODO: adjust for other formats, see img_fmt_r in madym_T1.schema.yaml
+        expand("{T1_dir}/{vols}{ext}",
+               T1_dir = config["T1_dir"],
+               vols = config["T1_vols"],
+               ext = [".nii.gz", ".json"])
+    output:
+        # TODO: adjust for other formats, see img_fmt_w in madym_T1.schema.yaml
+        expand("{output_dir}/{key}{ext}",
+               output_dir = config["output_dir"],
+               key = ["T1", "M0","efficiency"],
+               ext = [".xtr", ".nii.gz"]),
+        os.path.join(config["output_dir"], "error_tracker.nii.gz")
+        # touch(os.path.join(config["output_dir"], "madym_T1.done"))
+    log:
+        log = config["log_file"],
+        cfg = config["config_out"],
+        audit = os.path.join(config["audit_dir"], config["audit_name"])
+    script:
+       "../scripts/madym_T1.py"

workflow/schemas/madym_T1.schema.yaml

@@ -0,0 +1,121 @@
+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+
+# The following options are overriden by snakemake's functionality:
+# working_directory: set to workdir
+# config_file: disabled (replaced by rule's configfile)
+
+# roi_name
+
+properties:
+
+  # Inputs
+  T1_vols:
+    type: [array, "null"]
+    default: null
+    description: Variable flip angle file names, comma separated (no spaces).
+  T1_dir:
+    type: [string, "null"]
+    default: null
+    description: Folder containing T1 input volumes, can be left empty if already included in option --T1_vols
+  img_fmt_r:
+    type: string
+    default: NIFTI_GZ
+    # enum: [ANALYZE, ANALYZE_SPARSE, NIFTI, NIFTI_GZ, DICOM] # TODO: adjust madym_T1.smk inputs for other formats
+    const: NIFTI_GZ
+    description: Image format for reading input.
+  error_name:
+    type: [string, "null"]
+    default: null
+    description: Error codes image file name.
+
+  # Outputs
+  output_dir:
+    type: [string, "null"]
+    default: null
+    description: Output path, will use a temporary directory if empty.
+  img_fmt_w:
+    type: string
+    default: NIFTI_GZ
+    # enum: [ANALYZE, ANALYZE_SPARSE, NIFTI, NIFTI_GZ, DICOM] # TODO: adjust madym_T1.smk outputs for other formats
+    const: NIFTI_GZ
+    description: Image format for writing output.
+  log_file:
+    type: string
+    default: logs/madym_T1.log
+    description: Folder in which audit output is saved.
+  config_out:
+    type: [string, "null"]
+    default: logs/madym_T1.conf
+    description: Filename of the output config file.
+  no_log:
+    type: boolean
+    default: false
+    description: Switch off program logging.
+  no_audit:
+    type: boolean
+    default: true
+    description: Switch off audit logging.
+  audit_dir:
+    type: string
+    default: audit_logs
+    description: Folder in which audit output is saved.
+  audit_name:
+    type: string
+    default: madym_T1.audit
+    description: Audit file name.
+  quiet:
+    type: boolean
+    default: false
+    description: Do not display logging messages in cout.
+
+  # Params
+  method:
+    type: ["null","string"]
+    default: null
+    enum: [VFA, VFA_B1, IR, IR_E]
+    description: T1 method to use to fit, Variable Flip-Angle [B1 corrected], Inversion Recovery [with efficiency weighting]
+  B1_name:
+    type: [string, "null"]
+    default: null
+    description: Path to the B1 correction map.
+  B1_scaling:
+    type: ["number", "null"]
+    default: null
+    description: Value applied to scaled values in the B1 correction map.
+  B1_values:
+    type: [array, "null"]
+    default: null
+    description: B1 correction values, 1D array of length n_samples.
+  T1_noise:
+    type: ["number", "null"]
+    default: null
+    description: PD noise threshold.
+
+  # Other
+  nifti_scaling:
+    type: boolean
+    default: false
+    description: If set, applies intensity scaling and offset when reading/writing NIFTI images.
+  nifti_4D:
+    type: boolean
+    default: false
+    description: If set, reads NIFTI 4D images for T1 mapping and dynamic inputs.
+  use_BIDS:
+    type: boolean
+    default: false
+    description: If set, writes images using BIDS JSON meta info.
+  voxel_size_warn_only:
+    type: boolean
+    default: false
+    description: Warn if voxel sizes don't match for subsequent images.
+  overwrite:
+    type: boolean
+    default: true
+    description: Set overwrite existing analysis in the output directory ON.
+
+required:
+  - method
+  - T1_vols
+
+# additionalProperties: false

workflow/scripts/madym_T1.py

@@ -0,0 +1,87 @@
+import os
+import re
+
+from QbiMadym import madym_T1
+from QbiMadym.utils import local_madym_root
+
+import subprocess
+command = 'madym_T1.exe'
+try:
+    command = os.path.join(local_madym_root(),'madym_T1')
+    subprocess.run([command, "--version"], stdout = subprocess.PIPE, stderr = subprocess.PIPE, check=True)
+except subprocess.CalledProcessError:
+    raise NameError(f"{command} is not available.")
+
+madym_T1.run(
+    # 
+    working_directory = os.getcwd(),
+    config_file = None,
+    # cmd_exe = command,
+    # 
+    output_dir = snakemake.config["output_dir"],
+    img_fmt_w = "NIFTI_GZ",
+
+    # Input
+    # T1_dir = snakemake.config["T1_dir"],
+    T1_vols = [os.path.join(snakemake.config["T1_dir"], vol) for vol in snakemake.config["T1_vols"]],
+    img_fmt_r = "NIFTI_GZ",
+    roi_name = snakemake.config["roi_path"],
+    error_name = snakemake.config["error_name"],
+
+    # Params
+    method = snakemake.config["method"],
+    B1_name = snakemake.config["B1_name"],
+    B1_scaling = snakemake.config["B1_scaling"],
+    noise_thresh = snakemake.config["T1_noise"],
+    nifti_scaling = snakemake.config["nifti_scaling"],
+    nifti_4D = snakemake.config["nifti_4D"],
+    use_BIDS = snakemake.config["use_BIDS"],
+    voxel_size_warn_only = snakemake.config["voxel_size_warn_only"],
+    #
+    no_log = False,
+    quiet = False,
+    overwrite = True,
+    return_maps = False,
+    dummy_run = False,
+
+    no_audit = snakemake.config["no_audit"],
+    audit_dir = snakemake.config["audit_dir"],
+
+    program_log_name = "smk.log", # see below (*)
+    config_out = "smk.cfg",
+    audit_name = "smk.audit"
+
+    # madym_T1_lite options (not exposed)
+    #   ScannerParams = None,
+    #   signals = None,
+    #   TR = None,
+    #   B1_values = None,
+    #   output_name = 'madym_analysis.dat',
+)
+
+# (*) Logs are time-stamped and auto-renamed by madym:
+#
+#  {output_dir}/madym_T1_{date}_{time}_smk.log
+#  {output_dir}/madym_T1_{date}_{time}_smk.cfg
+#  {output_dir}/madym_T1_{date}_{time}_override_smk.cfg
+#  {audit_dir}/madym_T1_{date}_{time}_smk.audit
+#
+# Rename to consistent snakemake.log entries
+for item in snakemake.log.keys():
+
+    if item == "log" or item == "cfg":
+        dir = snakemake.config["output_dir"]
+    elif item == "audit":
+        dir = snakemake.config["audit_dir"]
+    else:
+        raise NameError("Unexpected log key: " + item)
+
+    for filename in os.listdir(dir):
+        match = re.match(r'madym_T1_(\d+)_(\d+)(_\w)?_smk\.' + item, filename)
+        if match:
+            if match.group(3) is None:
+                logname = snakemake.log[item]
+            else:
+                # Modify log.ext to e.g. log_override.ext
+                logname = re.sub(r'(\.\w+)$', match.group(3) + r'\1', snakemake.log[item])
+            os.rename(os.path.join(dir, filename), logname)