Refactor ADC calculation

[giladmaya]

Refactored ADC pre-processing command -

1. Fixed CLI input handling
2. Added missing click requirement
3. Wrap dicom reader/writer handling
4. Added warning messages

General

1. Added help to CLI parameters
2. Use click options to make CLI commands easier to use

[github-actions]

Coverage Report

File	Stmts	Miss	Cover	Missing
pd_dwi
__init__.py	2	0	100%
dataset.py	46	32	30%	12, 15–18, 20–22, 24, 26–27, 29, 31–32, 34–37, 39–43, 45, 47–49, 56, 59, 62, 66, 69
model.py	80	37	53%	56, 58–60, 62–63, 66, 68–70, 72–73, 77–78, 80–82, 84–85, 87–88, 90, 92–94, 100–111
training_utils.py	53	4	92%	27–28, 60, 84
pd_dwi/config
__init__.py	0	0	100%
config.py	71	1	98%	100
utils.py	11	1	90%	15
pd_dwi/dcm_utils
__init__.py	0	0	100%
reader.py	55	39	29%	8–11, 15–16, 18–23, 25–27, 29, 32–34, 36–40, 42–43, 45–46, 50–52, 54, 59–62, 66, 70, 74
tags.py	28	4	85%	7–8, 14, 17
writer.py	41	25	39%	17–18, 20–21, 24, 27, 30–31, 34, 36–37, 39–40, 43–44, 46, 48, 55–58, 61, 64, 67–68
pd_dwi/feature_selection
__init__.py	0	0	100%
select_k_best.py	6	0	100%
pd_dwi/models
__init__.py	12	4	66%	14–16, 18
pd_dwi/preprocessing
__init__.py	0	0	100%
adc.py	68	28	58%	21, 24, 26, 28–34, 36–37, 39, 42, 44, 46–51, 83–84, 86–87, 89, 91, 93
column_transformer.py	10	4	60%	14–15, 18, 20
pd_dwi/preprocessing/transformers
__init__.py	0	0	100%
hormone_receptor_encoder.py	19	9	52%	16–17, 19, 22–24, 26, 29, 32
radiomics_encoder.py	69	28	59%	40, 43, 55–56, 58, 61, 63–64, 66, 68, 71, 74, 77–82, 84–85, 87, 90, 93–98
sbr_grade_encoder.py	21	9	57%	18–19, 22, 24, 27–28, 30, 33, 36
pd_dwi/scripts
__init__.py	0	0	100%
adc_preprocess_command.py	27	17	37%	10–12, 22–25, 27, 29–30, 32–33, 35–36, 38–40
cli.py	19	0	100%
list_command.py	7	0	100%
predict_command.py	14	6	57%	16, 18–19, 21–22, 24
score_command.py	8	2	75%	11–12
train_command.py	10	3	70%	12–14
TOTAL	677	253	62%