Add Qbi runner refactor tool, and resulting config files & schemas

config/DCE_ETM.config.yaml

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+madym_config_file: null

config/DCE_VFA_T1_mapping.config.yaml

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+madym_config_file: null

config/DCE_deltaCt.config.yaml

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+
+# General (previously Qbi.runner options)
+#data_dir: null
+output_dir: logs/qMRI_processes
+# no_audit: True # -- this is a madym option
+
+# Inputs
+dce_path: dce/dce_dyn_echo1
+T1_path: madym_output/T1_VFA/T1.nii.gz
+
+dce_im_ext: .nii.gz
+dce_meta_ext: .json
+#roi_path: null
+
+# Parameters
+dce_limits: [2, 9, 11, 15] 
+relax_coeff: 0
+average_fun: median
+alternative: less
+equal_var: True
+
+# Output
+maps_dir: DCE_output_maps
+
+
+
+

config/OE_DCE_summary.config.yaml

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+summary_dir: 'summary_outputs'
+final_maps_dir: 'masked_maps'
+roi_masks_dir: 'roi_masks'
+suffixes: ['sig_5pct', 'sig_5pct_bf', 'sig_forman']

config/OE_IR_T1_mapping.config.yaml

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+madym_config_file: null

config/OE_deltaR1.config.yaml

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+roi_path: null
+oe_path: 'oxygen/oe'
+oe_im_ext: '.nii.gz'
+oe_meta_ext: '.json'
+oe_limits: null
+T1_path: 'madym_output/T1_IR/T1.nii.gz'
+efficiency_path: 'madym_output/T1_IR/efficiency.nii.gz'
+average_fun: 'median'
+alternative: 'less'
+equal_var: True
+sig_level: 0.05
+maps_dir: 'OE_output_maps'

dev/refactor_qbi_runner_parser.py

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+'''
+Take a python script.py with Qbi.runner.parser calls of the form:
+
+    parser.add('--param', type=str, default='foo', nargs=?, required=True,
+            help='description')
+    parser.add('--param2', type=int, default=42, nargs=3, help='description 2')
+
+Write a YAML config file script.config.yaml
+
+    param: 'foo'
+    param2: 42
+
+And a JSON-schema file script.schema.yaml
+
+    param:
+        type: string
+        default: 'foo'
+        description: 'description'
+        #required: True
+    param2:
+        type: integer
+        default: 42
+        description: 'description 2'
+        #nargs: 3
+'''
+import re
+import sys
+
+def replace_blocks(input_file, output_file, patterns, block_pattern = r'[\s\S]*'):
+
+    with open(input_file, 'r') as file:
+        content = file.read()
+
+    if isinstance(block_pattern, str):
+        block_pattern = (block_pattern,)
+
+    matches = re.finditer(block_pattern[0], content, re.MULTILINE | re.DOTALL)
+
+    content = ''
+    if matches:
+        for match in matches:
+
+            matched_text = match.group()
+
+            # Optional block substitution
+            if len(block_pattern) == 2:
+                matched_text = re.sub(block_pattern[0], block_pattern[1], matched_text)
+
+            # print(f'\n{matched_text}\n')
+
+            # Replace internal patterns
+            for old_pattern, new_pattern in patterns:
+                matched_text = re.sub(old_pattern, new_pattern, matched_text)
+
+                # print(f'old: {old_pattern}, new: {new_pattern}')
+                # print(f'\n{matched_text}\n')
+
+            # Replace the matched text in the original content
+            content = content + matched_text + '\n'
+
+        # print(content)
+
+        with open(output_file, 'w') as file:
+            file.write(content)
+
+        print(f'Replacements in {input_file} completed successfully.')
+    else:
+        print('No matches found for the specified block pattern.')
+
+if __name__ == "__main__":
+    if len(sys.argv) < 2:
+        print("Usage: python refactor_qbi_runner_parser.py <input_file>")
+        sys.exit(1)
+
+    input_file_path = sys.argv[1]
+
+    output_schema = re.sub(r'\.py$', r'.schema.yaml', input_file_path)
+    output_config = re.sub(r'\.py$', r'.config.yaml', input_file_path)
+
+    # Matches complete parser.add(...) call, keeps arguments only
+    block_pattern = (r'^\s*parser.add\(([\s\S]*?)\)$', r'\g<1>')
+
+    # Write configuration file with list: param: default
+    config_patterns = [
+        (r"\n\s+", r' '), # remove line breaks
+        (r"^'?--(\w*).*default=(\[[^]]*\]|'[^']*'|[^,)]*).*", r'\g<1>: \g<2>'), # --param, ..., default=foo
+        (r"^'?--(\w*).*", r'\g<1>: None')
+    ]
+    replace_blocks(input_file_path, output_config, config_patterns, block_pattern)
+
+    # Write schema with type, description, etc.
+    schema_patterns = [
+        (r"\n\s+", r' '), # remove line breaks
+        (r"^'?--(\w*)'?", r'\g<1>:'),                                       # --param
+        (r",\s*type=([^,)]*)", r'\n  type: \g<1>'),                         # type=foo
+        (r",\s*default=(\[[^]]*\]|'[^']*'|[^,)]*)", r'\n  default: \g<1>'),           # default=bar
+        (r",\s*help=('[^']*'|[^,)]*)", r'\n  description: \g<1>'),          # help='...'
+        (r",\s*nargs='\?'", r''),                                           # dump args='?'
+        (r",\s*(\w*)=('[^']*'|[^,)]*)", r'\n  #\g<1>: \g<2>'),              # comment everything else
+    ]
+    replace_blocks(input_file_path, output_schema, schema_patterns, block_pattern)
+
+    #
+    type_patterns = [
+        (r"  type: '?str'?", r'  type: string'),
+        (r"  type: '?int'?", r'  type: integer'),
+        (r"  type: '?float'?", r'  type: number'),
+        (r"  type: '?bool_option'?", r'  type: boolean')
+    ]
+    replace_blocks(output_schema, output_schema, type_patterns)

workflow/schemas/DCE_ETM.schema.yaml

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+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+description: foo
+
+properties:
+  madym_config_file:
+    type: string, required = False
+    description: ''
+
+

workflow/schemas/DCE_VFA_T1_mapping.schema.yaml

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+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+description: foo
+
+properties:
+  madym_config_file:
+    type: string, required = False
+    description: ''
+
+

workflow/schemas/DCE_deltaCt.schema.yaml

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+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+description: an entry in the sample sheet
+
+properties:
+  #General input arguments
+  data_dir:
+    type: string
+    description: 'Base data path'
+    default: './test'
+
+  roi_path:
+    type: ["null", string]
+    description: 'Relative path to roi mask file'
+    default: null
+
+  #Output dir
+  maps_dir:
+    type: string
+    description: 'Location of saved output maps, relative to data_dir'
+    default: 'DCE_output_maps'
+
+  #DCE input options
+  dce_path:
+    type: string
+    description: 'Relative path to DCE 4D-image volumes'
+    default: 'dynamic'
+
+  dce_im_ext:
+    type: string
+    description: 'File extension of the DCE volumes'
+    default: '.nii.gz'
+
+  dce_meta_ext:
+    type: string
+    description: 'File extension of the DCE volumes meta-info'
+    default: '.json'
+
+  dce_limits:
+    type: array
+    items:
+      type: integer
+    maxItems: 4
+    minItems: 4
+    description: 'Limits for the DCE volumes, 4 element integer list specifiying the timepoints for [baseline_start, baseline_, oxygen_start, oxygen_]'
+
+  T1_path:
+    type: string
+    description: 'Relative path to T1 image'
+    default: 'madym_output/T1_VFA/T1.nii.gz'
+
+  relax_coeff:
+    type: number
+    description: 'Relaxivity constant for contrast agent - units... '
+    default: 3.4
+
+  #Summary stats options
+  average_fun:
+    type: string
+    enum:
+      - median
+      - mean
+    description: 'Method used for temporal average {median, mean}.'
+    default: median
+
+  alternative:
+    type: string
+    enum:
+      - less
+      - two-sided
+      - greater
+    description: 'Apply 1-sided or 2-sided t-test: "less" = baseline lower than enhancing. Use "two-sided" for 2-sided.'
+    default: less
+
+  equal_var:
+    type: boolean
+    default: true 
+    description: 'Assume equal variance in pre/post enhancing periods'
+
+required:
+  - data_dir
+  - dce_limits

workflow/schemas/OE_DCE_hypoxia_mapping.schema.yaml

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+

workflow/schemas/OE_DCE_summary.schema.yaml

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+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+description: foo
+
+properties:
+  summary_dir:
+    type: string
+    default: 'summary_outputs'
+    description: ''
+  final_maps_dir:
+    type: string
+    default: 'masked_maps'
+    description: ''
+  roi_masks_dir:
+    type: string
+    default: 'roi_masks'
+    description: ''
+  suffixes:
+    type: string
+    #nargs: 3
+    default: ['sig_5pct', 'sig_5pct_bf', 'sig_forman']
+    description: ''
+
+

workflow/schemas/OE_IR_T1_mapping.schema.yaml

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+madym_config_file:
+  type: string, required = False
+  description: ''
+
+

workflow/schemas/OE_deltaR1.schema.yaml

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+$schema: "https://json-schema.org/draft/2020-12/schema"
+
+description: foo
+
+properties:
+  roi_path:
+    type: string
+    default: null
+    description: 'Relative path to roi mask file'
+  oe_path:
+    type: string
+    default: 'oxygen/oe'
+    description: 'Relative path to OE 4D-image volumes'
+  oe_im_ext:
+    type: string
+    default: '.nii.gz'
+    description: 'File extension of the OE volumes'
+  oe_meta_ext:
+    type: string
+    default: '.json'
+    description: 'File extension of the OE volumes meta-info'
+  oe_limits:
+    type: integer
+    #nargs: 4
+    #required: True
+    description: 'Limits for the OE volumes, 4 element integer list'
+  T1_path:
+    type: string
+    default: 'madym_output/T1_IR/T1.nii.gz'
+    description: 'Relative path to T1 image'
+  efficiency_path:
+    type: string
+    default: 'madym_output/T1_IR/efficiency.nii.gz'
+    description: 'Relative path to T1 efficiency image'
+  average_fun:
+    type: string
+    default: 'median'
+    description: 'Method used for temporal average {median, mean}.'
+  alternative:
+    type: string
+    default: 'less'
+    description: 'Apply 1-sided or 2-sided t-test: less = baseline lower than enhancing. Use "equal" for 2-sided.'
+  equal_var:
+    type: boolean
+    default: True,  const = True
+    description: 'Assume equal variance in pre/post enhancing periods'
+  sig_level:
+    type: number
+    default: 0.05
+    description: 'Significance level for p-value map thresholds'
+  maps_dir:
+    type: string
+    default: 'OE_output_maps'
+    description: 'Location of saved output maps, relative to data_dir'
+
+